From 2d2c9bec9a75f850b8d3bded98eeeb8e2ecb199f Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Thu, 7 May 2026 15:29:47 -0400 Subject: [PATCH 1/3] Vreation of the workflow to generate jbrowse2 instances with related species --- .../.dockstore.yml | 13 + .../CHANGELOG.md | 5 + ...ration-Jbrowse-tracks-alignments-tests.yml | 151 + .../Precuration-Jbrowse-tracks-alignments.ga | 3065 +++++++++++++++++ .../README.md | 70 + 5 files changed, 3304 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/.dockstore.yml create mode 100644 workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/CHANGELOG.md create mode 100644 workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml create mode 100644 workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga create mode 100644 workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/.dockstore.yml b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/.dockstore.yml new file mode 100644 index 0000000000..378998cbaf --- /dev/null +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/.dockstore.yml @@ -0,0 +1,13 @@ +version: 1.2 +workflows: +- name: main + subclass: Galaxy + publish: true + primaryDescriptorPath: /Precuration-Jbrowse-tracks-alignments.ga + testParameterFiles: + - /Precuration-Jbrowse-tracks-alignments-tests.yml + authors: + - name: Patrik Smeds + orcid: 0000-0001-6228-2785 + - name: Delphine Lariviere + orcid: 0000-0001-6421-3484 diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/CHANGELOG.md b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/CHANGELOG.md new file mode 100644 index 0000000000..9d6d3a2347 --- /dev/null +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/CHANGELOG.md @@ -0,0 +1,5 @@ +# Changelog + +## [0.1] - 2026-05-07 + +- Initial release: workflow generates JBrowse2 instances with assembly tracks (telomeres, gaps, coverage, optional gene annotation) and related-species alignments to assist manual curation of genome assemblies. Supports single- or dual-haplotype inputs. diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml new file mode 100644 index 0000000000..d66304fc26 --- /dev/null +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml @@ -0,0 +1,151 @@ +# Planemo test configuration for Jbrowse2 Precuration tracks workflow +# Test 1: Single haplotype with related species, no gene annotation +# Test 2: Two haplotypes with related species and gene annotation +# +# All test files are hosted on Zenodo record 20074725. The Q_telomeres input +# in the test reuses the P_telomeres file because the actual Q_telomeres test +# file is empty and cannot be uploaded to Zenodo. + +- doc: Test 1 - Single haplotype, related species, no gene annotation + job: + Species Name: Test_species + Assembly Name: toLID + Haplotype 1: + class: File + location: https://zenodo.org/records/20074725/files/Haplotype_1.fasta + filetype: fasta + hashes: + - hash_function: SHA-1 + hash_value: a0ee25fd9f7cf223ca40ff530e1201589fade212 + Will you use a second haplotype?: false + Related Species: + class: Collection + collection_type: list + elements: + - class: File + identifier: Related_species_1 + location: https://zenodo.org/records/20074725/files/Related_species_1.fasta.gz + filetype: fasta.gz + hashes: + - hash_function: SHA-1 + hash_value: 5121b574218ce9295fa6de1dd3fbdb1cfb9c68b1 + - class: File + identifier: Related_species_2 + location: https://zenodo.org/records/20074725/files/Related_species_2.fasta.gz + filetype: fasta.gz + hashes: + - hash_function: SHA-1 + hash_value: bd70fbde965e16ee88b54223d6dfe67989d3865f + Do you want to provide gene annotation for your assembly?: false + Telomere P: + class: File + location: https://zenodo.org/records/20074725/files/P_telomeres.bed + filetype: bed + hashes: + - hash_function: SHA-1 + hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d + Telomere Q: + class: File + location: https://zenodo.org/records/20074725/files/P_telomeres.bed + filetype: bed + hashes: + - hash_function: SHA-1 + hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d + Gaps: + class: File + location: https://zenodo.org/records/20074725/files/Gaps.bed + filetype: bed + hashes: + - hash_function: SHA-1 + hash_value: 5a14e6a11d9dc0ac41c3466f0693823a3f2c10be + Coverage: + class: File + location: https://zenodo.org/records/20074725/files/Coverage.bigwig + filetype: bigwig + hashes: + - hash_function: SHA-1 + hash_value: 63dfd14dbc162633ed123fc256dfc8ef756c5ad4 + outputs: + JBrowse2 Single Haplotype with related species: + element_tests: {} + JBrowse2 Single Haplotype with related species and Gene Tracks: + element_tests: {} + +- doc: Test 2 - Two haplotypes, related species, with gene annotation + job: + Species Name: Test_species + Assembly Name: toLID + Haplotype 1: + class: File + location: https://zenodo.org/records/20074725/files/Haplotype_1.fasta + filetype: fasta + hashes: + - hash_function: SHA-1 + hash_value: a0ee25fd9f7cf223ca40ff530e1201589fade212 + Will you use a second haplotype?: true + Haplotype 2: + class: File + location: https://zenodo.org/records/20074725/files/Haplotype_2.fasta + filetype: fasta + hashes: + - hash_function: SHA-1 + hash_value: 166cb118625113e39593bedb10aaea028c20f77d + Related Species: + class: Collection + collection_type: list + elements: + - class: File + identifier: Related_species_1 + location: https://zenodo.org/records/20074725/files/Related_species_1.fasta.gz + filetype: fasta.gz + hashes: + - hash_function: SHA-1 + hash_value: 5121b574218ce9295fa6de1dd3fbdb1cfb9c68b1 + - class: File + identifier: Related_species_2 + location: https://zenodo.org/records/20074725/files/Related_species_2.fasta.gz + filetype: fasta.gz + hashes: + - hash_function: SHA-1 + hash_value: bd70fbde965e16ee88b54223d6dfe67989d3865f + Do you want to provide gene annotation for your assembly?: true + Genes: + class: File + location: https://zenodo.org/records/20074725/files/Compleasm_genes_track.gff + filetype: gff3 + hashes: + - hash_function: SHA-1 + hash_value: 526abf443cc04c3904c2b2b140b19bb4f17622d0 + Telomere P: + class: File + location: https://zenodo.org/records/20074725/files/P_telomeres.bed + filetype: bed + hashes: + - hash_function: SHA-1 + hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d + Telomere Q: + class: File + location: https://zenodo.org/records/20074725/files/P_telomeres.bed + filetype: bed + hashes: + - hash_function: SHA-1 + hash_value: 54f67ca7cb77c89ce8b887ab0fa2205a69eec96d + Gaps: + class: File + location: https://zenodo.org/records/20074725/files/Gaps.bed + filetype: bed + hashes: + - hash_function: SHA-1 + hash_value: 5a14e6a11d9dc0ac41c3466f0693823a3f2c10be + Coverage: + class: File + location: https://zenodo.org/records/20074725/files/Coverage.bigwig + filetype: bigwig + hashes: + - hash_function: SHA-1 + hash_value: 63dfd14dbc162633ed123fc256dfc8ef756c5ad4 + outputs: + JBrowse2 Hap1 and hap2 with related species: + element_tests: {} + JBrowse2 Hap1 and hap2 with related species and gene tracks: + element_tests: {} diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga new file mode 100644 index 0000000000..2ac44485cb --- /dev/null +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga @@ -0,0 +1,3065 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "This Workflow generates Jbrowse2 Instances with genome assembly tracks and alignements agains related species to assist the manual curation of genome assemblies. ", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6228-2785", + "name": "Patrik Smeds" + }, + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6421-3484", + "name": "Delphine Lariviere" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "Jbrowse2 for Precuration with Related Species", + "readme": "", + "report": { + "markdown": "# Precuration workflow on:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Info\")\n```\n\n## Duplication Stats\n\nSamtools markdup deduplication stats (if applicable)\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats\")\n```\n\n\n\nPairtools stats\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats: MultiQC\")\n```\n\n## Telomere report\n\n```galaxy\nhistory_dataset_embedded(output=\"Telomere Report\")\n```\n\n## Pretext Snapshots\n\nWith Multimapping\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks - Multimapping\")\n```\n\n\nWith MAPQ filtering\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks\")\n```\n\n\n" + }, + "steps": { + "0": { + "annotation": "For Workflow report.", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "For Workflow report.", + "name": "Species Name" + } + ], + "label": "Species Name", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 0, + "top": 113.32852983289965 + }, + "tool_id": null, + "tool_state": "{\"multiple\": false, \"validators\": [], \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "fbb656ec-5dc2-4a7b-bb67-06642e707885", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "For Workflow report.", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "For Workflow report.", + "name": "Assembly Name" + } + ], + "label": "Assembly Name", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 95.65671993217956, + "top": 204.52575895443343 + }, + "tool_id": null, + "tool_state": "{\"multiple\": false, \"validators\": [], \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "dd9e5260-8f5e-42a9-8708-fe657736d107", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "Assembly for Haplotype 1.", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "Assembly for Haplotype 1.", + "name": "Haplotype 1" + } + ], + "label": "Haplotype 1", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 198.28766556712145, + "top": 333.06630818129815 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "fa895dbf-8f06-4728-ac6c-d526fcff2578", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Will you use a second haplotype?" + } + ], + "label": "Will you use a second haplotype?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 301.8902333217979, + "top": 405.0410156580133 + }, + "tool_id": null, + "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "697b66dc-1c0f-40d7-9d03-51318db580f1", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "Assembly for Haplotype 2. If \"Will you use a second haplotype?\" is set to \"no\", use haplotype 1 here. ", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "Assembly for Haplotype 2. If \"Will you use a second haplotype?\" is set to \"no\", use haplotype 1 here. ", + "name": "Haplotype 2" + } + ], + "label": "Haplotype 2", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 379.76112945636174, + "top": 508.0890158498388 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "b6516e91-ade5-457d-9b65-d54448413a13", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 454.5392171033154, + "top": 590.680154112835 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "ccac50f2-56b3-41ff-9670-4ef7e59dcd1d", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Do you want to provide gene annotation for your assembly?" + } + ], + "label": "Do you want to provide gene annotation for your assembly?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 542.4198438191992, + "top": 698.2369037827142 + }, + "tool_id": null, + "tool_state": "{\"default\": false, \"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "7b8f0c07-dc65-47c4-99c1-bf5d75d28ab2", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes" + } + ], + "label": "Genes", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 614.6440902431865, + "top": 818.8033806207972 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"gff3\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "fac0888a-e1fc-41df-b134-deb4b45d9a10", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomere Q" + } + ], + "label": "Telomere Q", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 680.5676592646699, + "top": 901.3563409388138 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "d535900a-9ab8-4860-9b0d-880b072c1aa6", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 9, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomere P" + } + ], + "label": "Telomere P", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 761.1770988870501, + "top": 998.8551768278469 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "aa5b2cfd-6a81-4e01-b721-2ff78cb1c8f9", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 10, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gaps" + } + ], + "label": "Gaps", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 816.7956506700089, + "top": 1085.617189755827 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "47b84649-e4a6-4e49-874b-b7194cd62167", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 11, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Coverage" + } + ], + "label": "Coverage", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 889.9015443268538, + "top": 1165.3201006570696 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "832bc0af-4341-470c-8da2-1ddbf94f83f0", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "errors": null, + "id": 12, + "input_connections": { + "components_0|param_type|component_value": { + "id": 0, + "output_name": "output" + }, + "components_2|param_type|component_value": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Compose text parameter value", + "outputs": [ + { + "name": "out1", + "type": "expression.json" + } + ], + "position": { + "left": 1513.3687877339703, + "top": 196.67349674870826 + }, + "post_job_actions": { + "HideDatasetActionout1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out1" + }, + "RenameDatasetActionout1": { + "action_arguments": { + "newname": "Assembly Info" + }, + "action_type": "RenameDatasetAction", + "output_name": "out1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", + "tool_shed_repository": { + "changeset_revision": "e188c9826e0f", + "name": "compose_text_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \": \"}}, {\"__index__\": 2, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.1", + "type": "tool", + "uuid": "b8f3cf11-2e38-4ad8-adaf-f73b48e4b2bf", + "when": null, + "workflow_outputs": [ + { + "label": "Assembly Info", + "output_name": "out1", + "uuid": "0c1bc167-f66b-4d07-9729-9c10669f6e02" + } + ] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 13, + "input_connections": { + "input_param_type|input_param": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": "Only one Haplotype", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 1696.2229666494914, + "top": 489.1299185816589 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": true, \"to\": \"False\"}, {\"__index__\": 1, \"from\": false, \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "66395547-21e9-4e70-bbe0-a8e14f361e65", + "when": null, + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 14, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 4, + "output_name": "output" + }, + "style_cond|type_cond|pick_from_1|value": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "data_param", + "type": "input" + } + ], + "position": { + "left": 1849.3268007633433, + "top": 762.524547165319 + }, + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "d1e92b9f-8bed-41b3-bbe8-f6e8c6f94fce", + "when": null, + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "content_id": "CONVERTER_gz_to_uncompressed", + "errors": null, + "id": 15, + "input_connections": { + "input1": { + "id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Convert gz compressed file to uncompressed.", + "outputs": [ + { + "name": "output1", + "type": "auto" + } + ], + "position": { + "left": 1782.0781695209464, + "top": 959.6837944877021 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput1": { + "action_arguments": { + "newtype": "fasta" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output1" + }, + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "tool_id": "CONVERTER_gz_to_uncompressed", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "3573f560-1fd1-4748-94f5-530c89717387", + "when": null, + "workflow_outputs": [] + }, + "16": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 16, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 7, + "output_name": "output" + }, + "style_cond|type_cond|pick_from_1|value": { + "id": 10, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "data_param", + "type": "input" + } + ], + "position": { + "left": 1889.2481070836782, + "top": 1357.6627147156235 + }, + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "15318e0e-6320-4637-a28b-29521d1c8d43", + "when": null, + "workflow_outputs": [] + }, + "17": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", + "errors": null, + "id": 17, + "input_connections": { + "infile": { + "id": 15, + "output_name": "output1" + } + }, + "inputs": [], + "label": null, + "name": "Search in textfiles", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 2193.787159776598, + "top": 516.9501479775356 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "tabular" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" + }, + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \">\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "4e84f6c9-53ca-4119-bfba-960c183e46b5", + "when": null, + "workflow_outputs": [] + }, + "18": { + "annotation": "", + "id": 18, + "input_connections": { + "Coverage": { + "id": 11, + "input_subworkflow_step_id": 5, + "output_name": "output" + }, + "Gaps": { + "id": 10, + "input_subworkflow_step_id": 4, + "output_name": "output" + }, + "Genes": { + "id": 16, + "input_subworkflow_step_id": 6, + "output_name": "data_param" + }, + "Genes?": { + "id": 6, + "input_subworkflow_step_id": 7, + "output_name": "output" + }, + "Hap1 fasta": { + "id": 2, + "input_subworkflow_step_id": 0, + "output_name": "output" + }, + "Related Species": { + "id": 15, + "input_subworkflow_step_id": 1, + "output_name": "output1" + }, + "Telomeres P": { + "id": 9, + "input_subworkflow_step_id": 3, + "output_name": "output" + }, + "Telomeres Q": { + "id": 8, + "input_subworkflow_step_id": 2, + "output_name": "output" + }, + "when": { + "id": 13, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": null, + "name": "Jbrowse for pre-curation single haplotype - 1 related Species ", + "outputs": [], + "position": { + "left": 2854.7399278462617, + "top": 1020.4253695653766 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "format-version": "0.1", + "name": "Jbrowse for pre-curation single haplotype - 1 related Species ", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 fasta" + } + ], + "label": "Hap1 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0.0, + "top": 229.96277645916257 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "4a20362f-2551-4a60-9118-e4c3e7c4f264", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 77.86825459522053, + "top": 325.6336833365997 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "771229b7-cdcc-462a-a1e5-314204a3fca1", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres Q" + } + ], + "label": "Telomeres Q", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 162.91806250869854, + "top": 456.26384063400747 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres P" + } + ], + "label": "Telomeres P", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 235.76054218223504, + "top": 579.8993537085871 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gaps" + } + ], + "label": "Gaps", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 325.8334374647798, + "top": 674.1406057066439 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Coverage" + } + ], + "label": "Coverage", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 426.80614784345863, + "top": 777.2141288680696 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "738f43fc-5f88-4117-bcc3-4a9c1b01c0a1", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes" + } + ], + "label": "Genes", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 481.54024694955143, + "top": 876.2540908741984 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "3831fc6f-0526-46ab-869b-5a07c6cded67", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes?" + } + ], + "label": "Genes?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 535.8872921148474, + "top": 982.3539279850593 + }, + "tool_id": null, + "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "bc1b0c8a-64af-4cac-a825-6eb7a70cbbeb", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "errors": null, + "id": 8, + "input_connections": { + "query": { + "id": 0, + "output_name": "output" + }, + "reflist": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": "hap1 vs species", + "name": "mashmap", + "outputs": [ + { + "name": "mashout", + "type": "paf" + } + ], + "position": { + "left": 865.3187502811058, + "top": 0 + }, + "post_job_actions": { + "HideDatasetActionmashout": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "mashout" + }, + "RenameDatasetActionmashout": { + "action_arguments": { + "newname": "hap1 vs species" + }, + "action_type": "RenameDatasetAction", + "output_name": "mashout" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a3a6b0b31f2d", + "name": "mashmap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"85.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.1.3+galaxy0", + "type": "tool", + "uuid": "b1a857dd-1140-4641-943b-cb141b6a6f81", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "Coverage": { + "id": 5, + "input_subworkflow_step_id": 6, + "output_name": "output" + }, + "Gaps": { + "id": 4, + "input_subworkflow_step_id": 5, + "output_name": "output" + }, + "Gene Tracks": { + "id": 6, + "input_subworkflow_step_id": 7, + "output_name": "output" + }, + "Genes?": { + "id": 7, + "input_subworkflow_step_id": 8, + "output_name": "output" + }, + "Hap1 fasta": { + "id": 0, + "input_subworkflow_step_id": 0, + "output_name": "output" + }, + "Hap1 vs Species": { + "id": 8, + "input_subworkflow_step_id": 2, + "output_name": "mashout" + }, + "Related Fasta": { + "id": 1, + "input_subworkflow_step_id": 1, + "output_name": "output" + }, + "Telomeres P": { + "id": 3, + "input_subworkflow_step_id": 4, + "output_name": "output" + }, + "Telomeres Q": { + "id": 2, + "input_subworkflow_step_id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Jbrowse2 for 1 related species - single haplotype", + "outputs": [], + "position": { + "left": 1523.302721783011, + "top": 447.47521325816376 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "format-version": "0.1", + "name": "Jbrowse2 for 1 related species - single haplotype", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 fasta" + } + ], + "label": "Hap1 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 209.22223652047438 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "4a20362f-2551-4a60-9118-e4c3e7c4f264", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Related Fasta" + } + ], + "label": "Related Fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 64.19044612855507, + "top": 339.63559170456904 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "385825a9-198e-425f-9fb3-55af892d20dc", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 vs Species" + } + ], + "label": "Hap1 vs Species", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 113.31939864522589, + "top": 479.1639618101156 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"paf\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "c18b3a25-89e8-4853-81fe-affb519a9ae0", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres Q" + } + ], + "label": "Telomeres Q", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 173.91872965677103, + "top": 640.6573469993632 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres P" + } + ], + "label": "Telomeres P", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 262.08020244071406, + "top": 799.4536221643712 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gaps" + } + ], + "label": "Gaps", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 334.3294215467986, + "top": 926.268574398666 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Coverage" + } + ], + "label": "Coverage", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 431.83941564925703, + "top": 1078.7178133506623 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "2131fd1e-4f34-4662-be5c-382101fcbc76", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gene Tracks" + } + ], + "label": "Gene Tracks", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 564.2214660523151, + "top": 1297.0956580243692 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "f6db855c-e1de-49f7-836c-87a510e955aa", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes?" + } + ], + "label": "Genes?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 676.3375507125828, + "top": 1426.4770174033545 + }, + "tool_id": null, + "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "a7391d09-c347-4520-91c2-8b07fd147efa", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 9, + "input_connections": { + "input_param_type|input_param": { + "id": 8, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": null, + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 1443.6518169393487, + "top": 980.4294207784309 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": true, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "216d68c5-1d97-4dc5-961a-ea915c97a92d", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 10, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 2, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 1, + "output_name": "output" + }, + "when": { + "id": 8, + "output_name": "output" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 and hap2 with 1st related species 2", + "name": "JBrowse2", + "outputs": [ + { + "name": "output", + "type": "html" + } + ], + "position": { + "left": 2561.3898434899743, + "top": 900.6399388618673 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Single Haplotype with related species and Gene Tracks" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": []}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "ffb776d2-dcb0-458c-9f2d-ffcd2de39ba2", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "output_name": "output", + "uuid": "a71b266a-4d49-4dbd-b4d1-410849b941bb" + } + ] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 11, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 2, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 1, + "output_name": "output" + }, + "when": { + "id": 9, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 and hap2 with 1st related species", + "name": "JBrowse2", + "outputs": [ + { + "name": "output", + "type": "html" + } + ], + "position": { + "left": 1931.9531666252099, + "top": 0 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Single Haplotype with related species" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": []}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "0dba1c5e-903c-46f3-a58c-2b9341b92a15", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype with related species", + "output_name": "output", + "uuid": "448fe2be-896a-49d7-b5c3-dfc4ceae0352" + } + ] + } + }, + "tags": [], + "uuid": "236c7163-dde8-4597-a9b5-a7d55314997e" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "6ad9fa44-c0d3-49e8-af09-e1a93e66eb8a", + "when": null, + "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype with related species", + "output_name": "JBrowse2 Single Haplotype with related species", + "uuid": "3c519fbb-453d-418c-8af3-e4532cf23c28" + }, + { + "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "uuid": "2dc05ed1-2c39-45a0-b07c-2ec4b8a6b0df" + } + ] + } + }, + "tags": [], + "uuid": "0569b4db-b204-41dc-b5c9-f5ad1b42265a" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "7fa40e11-ee9e-4492-852e-fa55278c26fe", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype with related species", + "output_name": "JBrowse2 Single Haplotype with related species", + "uuid": "3a5bf4bd-0e11-4289-b09a-3126d1da9594" + }, + { + "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "uuid": "77c9e164-d85b-454e-b996-29fe74100c03" + } + ] + }, + "19": { + "annotation": "", + "id": 19, + "input_connections": { + "Coverage": { + "id": 11, + "input_subworkflow_step_id": 6, + "output_name": "output" + }, + "Gaps": { + "id": 10, + "input_subworkflow_step_id": 5, + "output_name": "output" + }, + "Genes": { + "id": 16, + "input_subworkflow_step_id": 8, + "output_name": "data_param" + }, + "Genes?": { + "id": 6, + "input_subworkflow_step_id": 7, + "output_name": "output" + }, + "Hap1 fasta": { + "id": 2, + "input_subworkflow_step_id": 0, + "output_name": "output" + }, + "Hap2 fasta": { + "id": 14, + "input_subworkflow_step_id": 1, + "output_name": "data_param" + }, + "Related Species": { + "id": 15, + "input_subworkflow_step_id": 2, + "output_name": "output1" + }, + "Telomeres P": { + "id": 9, + "input_subworkflow_step_id": 4, + "output_name": "output" + }, + "Telomeres Q": { + "id": 8, + "input_subworkflow_step_id": 3, + "output_name": "output" + }, + "when": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Jbrowse for pre-curation", + "outputs": [], + "position": { + "left": 3359.99060088773, + "top": 782.0624564807059 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "format-version": "0.1", + "name": "Jbrowse for pre-curation", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 fasta" + } + ], + "label": "Hap1 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 85.5397415161874 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "4a20362f-2551-4a60-9118-e4c3e7c4f264", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap2 fasta" + } + ], + "label": "Hap2 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 51.81545453466647, + "top": 205.03846714316876 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "177f6825-e58e-45e9-a3fc-8c7623187e02", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 297.860981218189, + "top": 609.7270107228887 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "20f7abfb-20b8-49bb-b522-cd911fd1ec4c", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres Q" + } + ], + "label": "Telomeres Q", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 347.4491076529599, + "top": 765.9971383218501 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres P" + } + ], + "label": "Telomeres P", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 455.5329585464028, + "top": 870.0948319299273 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gaps" + } + ], + "label": "Gaps", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 524.1536909971493, + "top": 963.4615908089734 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Coverage" + } + ], + "label": "Coverage", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 581.1909253334677, + "top": 1050.5810577223672 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "738f43fc-5f88-4117-bcc3-4a9c1b01c0a1", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes?" + } + ], + "label": "Genes?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 632.8136499329014, + "top": 1153.233851898539 + }, + "tool_id": null, + "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "7c8dc365-9ea0-4f5a-af57-0983008b7ade", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes" + } + ], + "label": "Genes", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 683.9939626471161, + "top": 1243.3922887919446 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "dabdef6f-cb85-410c-a5ef-229d9ae21a3b", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "errors": null, + "id": 9, + "input_connections": { + "query": { + "id": 0, + "output_name": "output" + }, + "reflist": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": "Hap1 vs Species", + "name": "mashmap", + "outputs": [ + { + "name": "mashout", + "type": "paf" + } + ], + "position": { + "left": 1211.2240968936799, + "top": 0 + }, + "post_job_actions": { + "HideDatasetActionmashout": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "mashout" + }, + "RenameDatasetActionmashout": { + "action_arguments": { + "newname": "Species to Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "mashout" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a3a6b0b31f2d", + "name": "mashmap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"85.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.1.3+galaxy0", + "type": "tool", + "uuid": "ba8fe065-a989-4cff-bcda-2e6883b1f6cd", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "errors": null, + "id": 10, + "input_connections": { + "query": { + "id": 2, + "output_name": "output" + }, + "reflist": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": "Species vs Hap2", + "name": "mashmap", + "outputs": [ + { + "name": "mashout", + "type": "paf" + } + ], + "position": { + "left": 1225.3530086334274, + "top": 365.8375864791642 + }, + "post_job_actions": { + "HideDatasetActionmashout": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "mashout" + }, + "RenameDatasetActionmashout": { + "action_arguments": { + "newname": "Species to Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "mashout" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a3a6b0b31f2d", + "name": "mashmap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"85.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.1.3+galaxy0", + "type": "tool", + "uuid": "cf1e95b5-3bd6-41c1-a2d4-93ac6c1b1b1a", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": { + "Coverage": { + "id": 6, + "input_subworkflow_step_id": 8, + "output_name": "output" + }, + "Gaps": { + "id": 5, + "input_subworkflow_step_id": 7, + "output_name": "output" + }, + "Genes": { + "id": 8, + "input_subworkflow_step_id": 10, + "output_name": "output" + }, + "Genes?": { + "id": 7, + "input_subworkflow_step_id": 9, + "output_name": "output" + }, + "Hap1 fasta": { + "id": 0, + "input_subworkflow_step_id": 0, + "output_name": "output" + }, + "Hap1 vs Species": { + "id": 9, + "input_subworkflow_step_id": 4, + "output_name": "mashout" + }, + "Hap2 fasta": { + "id": 1, + "input_subworkflow_step_id": 1, + "output_name": "output" + }, + "Related Species": { + "id": 2, + "input_subworkflow_step_id": 2, + "output_name": "output" + }, + "Species vs Hap2": { + "id": 10, + "input_subworkflow_step_id": 3, + "output_name": "mashout" + }, + "Telomeres P": { + "id": 4, + "input_subworkflow_step_id": 6, + "output_name": "output" + }, + "Telomeres Q": { + "id": 3, + "input_subworkflow_step_id": 5, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Jbrowse2 for 1 related species", + "outputs": [], + "position": { + "left": 2292.870790775461, + "top": 343.7939440488241 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "format-version": "0.1", + "name": "Jbrowse2 for 1 related species", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 fasta" + } + ], + "label": "Hap1 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 271.13908772215916 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "4a20362f-2551-4a60-9118-e4c3e7c4f264", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap2 fasta" + } + ], + "label": "Hap2 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 53.14881800970572, + "top": 420.7641795440555 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "177f6825-e58e-45e9-a3fc-8c7623187e02", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 98.91709918730632, + "top": 553.1054764799819 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "604a6bec-8c1f-47e3-8884-c32f63246589", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Species vs Hap2" + } + ], + "label": "Species vs Hap2", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 147.9198303415696, + "top": 670.2931389328182 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"paf\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ebdc47b3-16f5-48e9-a101-c82b2370181a", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 vs Species" + } + ], + "label": "Hap1 vs Species", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 175.64670268098203, + "top": 777.2105888619357 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"paf\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "385825a9-198e-425f-9fb3-55af892d20dc", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres Q" + } + ], + "label": "Telomeres Q", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 206.21568172170709, + "top": 895.0983900914266 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres P" + } + ], + "label": "Telomeres P", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 274.77222990165984, + "top": 1069.4502766623036 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gaps" + } + ], + "label": "Gaps", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 353.8919295731858, + "top": 1244.9653893778952 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Coverage" + } + ], + "label": "Coverage", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 391.49614814580605, + "top": 1410.3962329181184 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "2131fd1e-4f34-4662-be5c-382101fcbc76", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 9, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes?" + } + ], + "label": "Genes?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 419.6781495431659, + "top": 1559.6965461441787 + }, + "tool_id": null, + "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "ccb4de54-c370-4f56-a5d4-42708ee6c835", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 10, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes" + } + ], + "label": "Genes", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 450.73254127706855, + "top": 1696.059196784704 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "496c7358-def1-4256-b4e8-6698cac34f97", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 11, + "input_connections": { + "input_param_type|input_param": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": "No Gene track", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 1030.3127513910322, + "top": 1346.1174612746302 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": false, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "d8f71bf4-51a3-4af7-8cf2-fd16730469b4", + "when": null, + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 12, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "output" + }, + "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 10, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 2, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_2|reference_genome|genome": { + "id": 1, + "output_name": "output" + }, + "assemblies_2|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_2|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_2|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_2|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "output" + }, + "assemblies_2|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 10, + "output_name": "output" + }, + "when": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "name": "JBrowse2", + "outputs": [ + { + "name": "output", + "type": "html" + } + ], + "position": { + "left": 2604.560544371787, + "top": 306.40203071991476 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Hap1 and hap2 with related species and gene tracks" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 2, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres Haplotype 2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "c4b25ca4-bdd4-4260-ac8b-80ae381da1ab", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "output_name": "output", + "uuid": "78b83679-2eea-4812-9936-54e27a2c404d" + } + ] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 13, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 2, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_2|reference_genome|genome": { + "id": 1, + "output_name": "output" + }, + "assemblies_2|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_2|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_2|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_2|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "output" + }, + "when": { + "id": 11, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 and hap2 with 1st related species", + "name": "JBrowse2", + "outputs": [ + { + "name": "output", + "type": "html" + } + ], + "position": { + "left": 1960.7191746063156, + "top": 0 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Hap1 and hap2 with related species" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 2, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres Haplotype 2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "0dba1c5e-903c-46f3-a58c-2b9341b92a15", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 and hap2 with related species", + "output_name": "output", + "uuid": "ce6026de-ad8b-4dec-8926-fccc97f25df6" + } + ] + } + }, + "tags": [], + "uuid": "fb028d13-e1d0-4d81-b413-b2c662d5213a" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "e134915a-f5b7-4b32-a511-921e0b363bff", + "when": null, + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 and hap2 with related species", + "output_name": "JBrowse2 Hap1 and hap2 with related species", + "uuid": "7562c81f-4b86-4932-8056-52f4dc17d2a9" + }, + { + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "uuid": "ca3249af-b46a-450d-8dbe-696490325d42" + } + ] + } + }, + "tags": [], + "uuid": "ef9af3c8-a765-4077-9cb2-9ad16d1a570e" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "af188630-081d-489b-b46f-eae324b3df01", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 and hap2 with related species", + "output_name": "JBrowse2 Hap1 and hap2 with related species", + "uuid": "6861e850-7a02-47cf-aab2-4093019878e9" + }, + { + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "uuid": "edb52be2-a128-49cb-9c82-e693d7b7656c" + } + ] + }, + "20": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", + "errors": null, + "id": 20, + "input_connections": { + "input_list": { + "id": 17, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Collapse Collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 2499.556473225303, + "top": 293.47025968475924 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", + "tool_shed_repository": { + "changeset_revision": "90981f86000f", + "name": "collapse_collections", + "owner": "nml", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "5.1.0", + "type": "tool", + "uuid": "c70c2d41-43fe-4601-a3aa-8ca8a5433c0a", + "when": null, + "workflow_outputs": [] + }, + "21": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy3", + "errors": null, + "id": 21, + "input_connections": { + "infile": { + "id": 20, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Unique", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 2853.562857058991, + "top": 0.0 + }, + "post_job_actions": { + "ChangeDatatypeActionoutfile": { + "action_arguments": { + "newtype": "tabular" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "outfile" + }, + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "19ffba37-86b9-4fe3-aae8-f8fbfa2d4ff0", + "when": null, + "workflow_outputs": [] + }, + "22": { + "annotation": "", + "content_id": "wc_gnu", + "errors": null, + "id": 22, + "input_connections": { + "input1": { + "id": 20, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Line/Word/Character count", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 2812.55061813865, + "top": 510.6734558790175 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "wc_gnu", + "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "b00153cb-f706-4e4a-bda6-4b3e859858f6", + "when": null, + "workflow_outputs": [] + }, + "23": { + "annotation": "", + "content_id": "wc_gnu", + "errors": null, + "id": 23, + "input_connections": { + "input1": { + "id": 21, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Line/Word/Character count", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 3066.1573769206448, + "top": 268.5825615907663 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "wc_gnu", + "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "b1b48543-f5a6-410b-aeb6-86c058dee9e3", + "when": null, + "workflow_outputs": [] + }, + "24": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 24, + "input_connections": { + "input1": { + "id": 22, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 3236.7131866213954, + "top": 502.9407403932288 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "0d89e2e9-fec0-4bc8-a3fc-513dc91f2f1b", + "when": null, + "workflow_outputs": [] + }, + "25": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 25, + "input_connections": { + "input1": { + "id": 23, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 3349.6578232069623, + "top": 103.77316093552422 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "9f9a8b3d-6d0a-424f-aae0-4db2e0c16940", + "when": null, + "workflow_outputs": [] + }, + "26": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "errors": null, + "id": 26, + "input_connections": { + "components_0|param_type|component_value": { + "id": 24, + "output_name": "integer_param" + }, + "components_1|param_type|component_value": { + "id": 25, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Calculate numeric parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 3600.8912340886463, + "top": 332.9150842713157 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "tool_shed_repository": { + "changeset_revision": "0e586762f97b", + "name": "calculate_numeric_param", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"-\"}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"\"}], \"output_type\": \"integer\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "34cce52f-7548-4454-94ad-ee1547b25636", + "when": null, + "workflow_outputs": [] + }, + "27": { + "annotation": "This step is meant to warn the user that there are duplicated sequence names, which would cause inaccurate alignments results with MashMap. ", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 27, + "input_connections": { + "input_param_type|input_param": { + "id": 26, + "output_name": "integer_param" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": "Fail if there are duplicated sequence names between the fasta files", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 3822.4432951091107, + "top": 766.5545148192659 + }, + "post_job_actions": { + "RenameDatasetActionoutput_param_boolean": { + "action_arguments": { + "newname": "Fail if there are duplicated sequence names between the fasta files" + }, + "action_type": "RenameDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"integer\", \"__current_case__\": 1, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"0\", \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "84eeffe0-4578-4857-8555-841769a58073", + "when": null, + "workflow_outputs": [ + { + "label": "Fail if there are duplicated sequence names between the fasta files", + "output_name": "output_param_boolean", + "uuid": "b4ebfb36-d369-4ced-964c-450c62e01b7d" + } + ] + } + }, + "tags": [], + "uuid": "2e394d56-6c89-4588-956e-5c1a9abd33c2", + "version": 1, + "release": "0.1" +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md new file mode 100644 index 0000000000..a3251b683a --- /dev/null +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md @@ -0,0 +1,70 @@ +# JBrowse2 Precuration Tracks with Related Species Alignments + +This workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species. + +The workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser. + +## Inputs + +### Required Inputs + +1. **Species Name** [text] - Species identifier used in the assembly info report +2. **Assembly Name** [text] - Assembly identifier (e.g., toLID) +3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names) +4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies +5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes) +6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`). +7. **Telomere P** [BED] - P-arm telomere coordinates +8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty) +9. **Gaps** [BED] - Assembly gap coordinates +10. **Coverage** [BigWig] - PacBio HiFi read coverage track + +### Gene Annotation Options + +11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance +12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled) + +## Outputs + +1. **Assembly Info** - Summary of species and assembly name +2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used) +3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included +4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used) +5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included + +## Usage Notes + +### Pairing with the Hi-C contact map workflow + +This workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow: + +| Hi-C workflow output | Use here as input | +|---|---| +| `Decontaminated Hap1 with Suffix` | `Haplotype 1` | +| `Decontaminated Hap2 with Suffix` | `Haplotype 2` | +| `P telomeres bed` | `Telomere P` | +| `Q telomeres Bed` | `Telomere Q` | +| `Gaps Bed` | `Gaps` | +| `BigWig Coverage` | `Coverage` | +| `Compleasm Genes track` | `Genes` | + +### Related species selection + +Choose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection. + +**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example: + +```bash +zcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz +``` + +### Scaffold name suffixes + +If using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks. + +## Citation + +If you use this workflow, please cite: +- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z)) +- minimap2 (used for related-species alignment) +- Other tools as listed in the workflow From 3ea97a596b44ffa2ac78e0070b190aacfa96cead Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Tue, 12 May 2026 17:53:44 -0400 Subject: [PATCH 2/3] add Jbrowse with no haplotypes here instead of the precuration workflow --- ...ration-Jbrowse-tracks-alignments-tests.yml | 8 + .../Precuration-Jbrowse-tracks-alignments.ga | 907 ++++++++++++++---- .../README.md | 13 + 3 files changed, 727 insertions(+), 201 deletions(-) diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml index d66304fc26..6d8f198073 100644 --- a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml @@ -66,6 +66,10 @@ - hash_function: SHA-1 hash_value: 63dfd14dbc162633ed123fc256dfc8ef756c5ad4 outputs: + JBrowse2 Single Haplotype: + asserts: + has_text: + text: "JBrowse" JBrowse2 Single Haplotype with related species: element_tests: {} JBrowse2 Single Haplotype with related species and Gene Tracks: @@ -145,6 +149,10 @@ - hash_function: SHA-1 hash_value: 63dfd14dbc162633ed123fc256dfc8ef756c5ad4 outputs: + JBrowse2 Hap1 vs Hap2 with gene tracks: + asserts: + has_text: + text: "JBrowse" JBrowse2 Hap1 and hap2 with related species: element_tests: {} JBrowse2 Hap1 and hap2 with related species and gene tracks: diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga index 2ac44485cb..4d82d0aafe 100644 --- a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "This Workflow generates Jbrowse2 Instances with genome assembly tracks and alignements agains related species to assist the manual curation of genome assemblies. ", + "annotation": "This workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species to assist the manual curation of genome assemblies. ", "comments": [], "creator": [ { @@ -16,8 +16,8 @@ ], "format-version": "0.1", "license": "MIT", + "release": "0.1", "name": "Jbrowse2 for Precuration with Related Species", - "readme": "", "report": { "markdown": "# Precuration workflow on:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Info\")\n```\n\n## Duplication Stats\n\nSamtools markdup deduplication stats (if applicable)\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats\")\n```\n\n\n\nPairtools stats\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats: MultiQC\")\n```\n\n## Telomere report\n\n```galaxy\nhistory_dataset_embedded(output=\"Telomere Report\")\n```\n\n## Pretext Snapshots\n\nWith Multimapping\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks - Multimapping\")\n```\n\n\nWith MAPQ filtering\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks\")\n```\n\n\n" }, @@ -45,7 +45,7 @@ "tool_state": "{\"multiple\": false, \"validators\": [], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "fbb656ec-5dc2-4a7b-bb67-06642e707885", + "uuid": "61d68c28-9135-4fb7-af7f-6cf04e88cc9a", "when": null, "workflow_outputs": [] }, @@ -72,7 +72,7 @@ "tool_state": "{\"multiple\": false, \"validators\": [], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "dd9e5260-8f5e-42a9-8708-fe657736d107", + "uuid": "8cc23e0a-d9bb-429c-a08e-ca357b3c3ad9", "when": null, "workflow_outputs": [] }, @@ -99,7 +99,7 @@ "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "fa895dbf-8f06-4728-ac6c-d526fcff2578", + "uuid": "672ebc11-5a2e-427c-9b64-c811821b5768", "when": null, "workflow_outputs": [] }, @@ -126,7 +126,7 @@ "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "697b66dc-1c0f-40d7-9d03-51318db580f1", + "uuid": "1f933849-8bc5-47ff-83da-7f53006c39cf", "when": null, "workflow_outputs": [] }, @@ -146,49 +146,22 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 379.76112945636174, - "top": 508.0890158498388 + "left": 415.3930839522133, + "top": 539.8438023368923 }, "tool_id": null, "tool_state": "{\"optional\": true, \"format\": [\"fasta\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "b6516e91-ade5-457d-9b65-d54448413a13", + "uuid": "12c55b92-9015-4d4d-97ee-b675971486e4", "when": null, "workflow_outputs": [] }, "5": { - "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", - "content_id": null, - "errors": null, - "id": 5, - "input_connections": {}, - "inputs": [ - { - "description": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", - "name": "Related Species" - } - ], - "label": "Related Species", - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": 454.5392171033154, - "top": 590.680154112835 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", - "tool_version": null, - "type": "data_collection_input", - "uuid": "ccac50f2-56b3-41ff-9670-4ef7e59dcd1d", - "when": null, - "workflow_outputs": [] - }, - "6": { "annotation": "", "content_id": null, "errors": null, - "id": 6, + "id": 5, "input_connections": {}, "inputs": [ { @@ -200,22 +173,22 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 542.4198438191992, - "top": 698.2369037827142 + "left": 532.8506745873698, + "top": 662.309181460891 }, "tool_id": null, "tool_state": "{\"default\": false, \"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "7b8f0c07-dc65-47c4-99c1-bf5d75d28ab2", + "uuid": "ae28b111-3e2f-4506-b653-97b4cebcee72", "when": null, "workflow_outputs": [] }, - "7": { + "6": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 6, "input_connections": {}, "inputs": [ { @@ -234,15 +207,15 @@ "tool_state": "{\"optional\": true, \"format\": [\"gff3\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "fac0888a-e1fc-41df-b134-deb4b45d9a10", + "uuid": "5983756f-c13c-4a41-b323-f52db5e172a4", "when": null, "workflow_outputs": [] }, - "8": { + "7": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 7, "input_connections": {}, "inputs": [ { @@ -261,15 +234,15 @@ "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "d535900a-9ab8-4860-9b0d-880b072c1aa6", + "uuid": "1b1bf84f-e625-4b7d-8f9e-471cd5a18b4c", "when": null, "workflow_outputs": [] }, - "9": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 8, "input_connections": {}, "inputs": [ { @@ -288,15 +261,15 @@ "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "aa5b2cfd-6a81-4e01-b721-2ff78cb1c8f9", + "uuid": "6e214300-bac1-46e2-9dba-b305b10dbe28", "when": null, "workflow_outputs": [] }, - "10": { + "9": { "annotation": "", "content_id": null, "errors": null, - "id": 10, + "id": 9, "input_connections": {}, "inputs": [ { @@ -315,15 +288,15 @@ "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "47b84649-e4a6-4e49-874b-b7194cd62167", + "uuid": "04f38367-909b-4c7b-a452-261dcc1b77da", "when": null, "workflow_outputs": [] }, - "11": { + "10": { "annotation": "", "content_id": null, "errors": null, - "id": 11, + "id": 10, "input_connections": {}, "inputs": [ { @@ -342,7 +315,34 @@ "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "832bc0af-4341-470c-8da2-1ddbf94f83f0", + "uuid": "67d4f124-7ba7-4ca8-9980-77efb986ad53", + "when": null, + "workflow_outputs": [] + }, + "11": { + "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "content_id": null, + "errors": null, + "id": 11, + "input_connections": {}, + "inputs": [ + { + "description": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 1016.2648364611407, + "top": 1255.890937169875 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "b1d57707-483c-43cd-8256-0a2888af1246", "when": null, "workflow_outputs": [] }, @@ -399,13 +399,13 @@ "tool_uuid": null, "tool_version": "0.1.1", "type": "tool", - "uuid": "b8f3cf11-2e38-4ad8-adaf-f73b48e4b2bf", + "uuid": "e8e6b489-fa33-4563-ba7a-9978b88c22e2", "when": null, "workflow_outputs": [ { "label": "Assembly Info", "output_name": "out1", - "uuid": "0c1bc167-f66b-4d07-9729-9c10669f6e02" + "uuid": "9bc7a768-762d-4578-b675-7656de8d8a65" } ] }, @@ -420,12 +420,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map parameter value", - "name": "input_param_type" - } - ], + "inputs": [], "label": "Only one Haplotype", "name": "Map parameter value", "outputs": [ @@ -435,8 +430,8 @@ } ], "position": { - "left": 1696.2229666494914, - "top": 489.1299185816589 + "left": 1736.3581103638398, + "top": 455.0639514218991 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -456,7 +451,7 @@ "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "66395547-21e9-4e70-bbe0-a8e14f361e65", + "uuid": "df19ed91-a001-4caa-91f8-8d9051fde5c9", "when": null, "workflow_outputs": [] }, @@ -485,8 +480,8 @@ } ], "position": { - "left": 1849.3268007633433, - "top": 762.524547165319 + "left": 1706.8744833487017, + "top": 654.7944887566696 }, "post_job_actions": { "HideDatasetActiondata_param": { @@ -506,104 +501,104 @@ "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "d1e92b9f-8bed-41b3-bbe8-f6e8c6f94fce", + "uuid": "e6631462-b13d-46f1-8fdd-a3e760c3f76a", "when": null, "workflow_outputs": [] }, "15": { "annotation": "", - "content_id": "CONVERTER_gz_to_uncompressed", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, "id": 15, "input_connections": { - "input1": { - "id": 5, + "style_cond|type_cond|pick_from_0|value": { + "id": 6, + "output_name": "output" + }, + "style_cond|type_cond|pick_from_1|value": { + "id": 9, "output_name": "output" } }, "inputs": [], "label": null, - "name": "Convert gz compressed file to uncompressed.", + "name": "Pick parameter value", "outputs": [ { - "name": "output1", - "type": "auto" + "name": "data_param", + "type": "input" } ], "position": { - "left": 1782.0781695209464, - "top": 959.6837944877021 + "left": 2050.977397800029, + "top": 1042.9931586846508 }, "post_job_actions": { - "ChangeDatatypeActionoutput1": { - "action_arguments": { - "newtype": "fasta" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "output1" - }, - "HideDatasetActionoutput1": { + "HideDatasetActiondata_param": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "output1" + "output_name": "data_param" } }, - "tool_id": "CONVERTER_gz_to_uncompressed", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.0.0", + "tool_version": "0.2.0", "type": "tool", - "uuid": "3573f560-1fd1-4748-94f5-530c89717387", + "uuid": "87a497ce-176b-4e85-adf2-0f3e58b24670", "when": null, "workflow_outputs": [] }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "content_id": "CONVERTER_gz_to_uncompressed", "errors": null, "id": 16, "input_connections": { - "style_cond|type_cond|pick_from_0|value": { - "id": 7, - "output_name": "output" - }, - "style_cond|type_cond|pick_from_1|value": { - "id": 10, + "input1": { + "id": 11, "output_name": "output" } }, "inputs": [], "label": null, - "name": "Pick parameter value", + "name": "Convert gz compressed file to uncompressed.", "outputs": [ { - "name": "data_param", - "type": "input" + "name": "output1", + "type": "auto" } ], "position": { - "left": 1889.2481070836782, - "top": 1357.6627147156235 + "left": 1685.3438207068607, + "top": 928.4985122876616 }, "post_job_actions": { - "HideDatasetActiondata_param": { + "ChangeDatatypeActionoutput1": { + "action_arguments": { + "newtype": "fasta" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output1" + }, + "HideDatasetActionoutput1": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "data_param" + "output_name": "output1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", - "tool_shed_repository": { - "changeset_revision": "b19e21af9c52", - "name": "pick_value", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_id": "CONVERTER_gz_to_uncompressed", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.2.0", + "tool_version": "1.0.0", "type": "tool", - "uuid": "15318e0e-6320-4637-a28b-29521d1c8d43", + "uuid": "6f868700-ff9c-4415-98d7-81befe9dde9e", "when": null, "workflow_outputs": [] }, @@ -614,7 +609,7 @@ "id": 17, "input_connections": { "infile": { - "id": 15, + "id": 16, "output_name": "output1" } }, @@ -656,7 +651,7 @@ "tool_uuid": null, "tool_version": "9.5+galaxy3", "type": "tool", - "uuid": "4e84f6c9-53ca-4119-bfba-960c183e46b5", + "uuid": "24671126-d835-4ecf-94c6-f22fa01d6abd", "when": null, "workflow_outputs": [] }, @@ -665,22 +660,22 @@ "id": 18, "input_connections": { "Coverage": { - "id": 11, + "id": 10, "input_subworkflow_step_id": 5, "output_name": "output" }, "Gaps": { - "id": 10, + "id": 9, "input_subworkflow_step_id": 4, "output_name": "output" }, "Genes": { - "id": 16, + "id": 15, "input_subworkflow_step_id": 6, "output_name": "data_param" }, "Genes?": { - "id": 6, + "id": 5, "input_subworkflow_step_id": 7, "output_name": "output" }, @@ -690,17 +685,17 @@ "output_name": "output" }, "Related Species": { - "id": 15, + "id": 16, "input_subworkflow_step_id": 1, "output_name": "output1" }, "Telomeres P": { - "id": 9, + "id": 8, "input_subworkflow_step_id": 3, "output_name": "output" }, "Telomeres Q": { - "id": 8, + "id": 7, "input_subworkflow_step_id": 2, "output_name": "output" }, @@ -714,8 +709,8 @@ "name": "Jbrowse for pre-curation single haplotype - 1 related Species ", "outputs": [], "position": { - "left": 2854.7399278462617, - "top": 1020.4253695653766 + "left": 2934.6624331027892, + "top": 744.4198856816727 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -743,8 +738,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, - "top": 229.96277645916257 + "left": 0, + "top": 699.2443289019618 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -771,7 +766,7 @@ "outputs": [], "position": { "left": 77.86825459522053, - "top": 325.6336833365997 + "top": 794.9152357793989 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", @@ -798,7 +793,7 @@ "outputs": [], "position": { "left": 162.91806250869854, - "top": 456.26384063400747 + "top": 925.5453930768067 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", @@ -825,7 +820,7 @@ "outputs": [], "position": { "left": 235.76054218223504, - "top": 579.8993537085871 + "top": 1049.1809061513864 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", @@ -852,7 +847,7 @@ "outputs": [], "position": { "left": 325.8334374647798, - "top": 674.1406057066439 + "top": 1143.422158149443 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", @@ -879,7 +874,7 @@ "outputs": [], "position": { "left": 426.80614784345863, - "top": 777.2141288680696 + "top": 1246.4956813108688 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", @@ -906,7 +901,7 @@ "outputs": [], "position": { "left": 481.54024694955143, - "top": 876.2540908741984 + "top": 1345.5356433169977 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -933,7 +928,7 @@ "outputs": [], "position": { "left": 535.8872921148474, - "top": 982.3539279850593 + "top": 1451.6354804278585 }, "tool_id": null, "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", @@ -968,8 +963,8 @@ } ], "position": { - "left": 865.3187502811058, - "top": 0 + "left": 1026.595772250997, + "top": 858.7635819182626 }, "post_job_actions": { "HideDatasetActionmashout": { @@ -1002,7 +997,131 @@ }, "9": { "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, "id": 9, + "input_connections": { + "input_param_type|input_param": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 909.3164880438957, + "top": 1632.3549251437048 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": true, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "a8eddf6e-6019-46b9-bda4-3cae4f66baf1", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 10, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 2, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "when": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 with gene track", + "name": "JBrowse2", + "outputs": [ + { + "name": "output", + "type": "html" + } + ], + "position": { + "left": 1896.9114798587966, + "top": 990.3320527378663 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Single Haplotype with Gene Track" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "8244bcfd-113f-4a5f-8b7a-4ebf39a2fd0d", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype with Gene Track", + "output_name": "output", + "uuid": "b4b0f191-314c-4519-8ea9-6885a3c3a1e5" + } + ] + }, + "11": { + "annotation": "", + "id": 11, "input_connections": { "Coverage": { "id": 5, @@ -1055,8 +1174,8 @@ "name": "Jbrowse2 for 1 related species - single haplotype", "outputs": [], "position": { - "left": 1523.302721783011, - "top": 447.47521325816376 + "left": 1504.531864079652, + "top": 1218.259001224898 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1322,12 +1441,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map parameter value", - "name": "input_param_type" - } - ], + "inputs": [], "label": null, "name": "Map parameter value", "outputs": [ @@ -1539,36 +1653,120 @@ "uuid": "6ad9fa44-c0d3-49e8-af09-e1a93e66eb8a", "when": null, "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "uuid": "2dc05ed1-2c39-45a0-b07c-2ec4b8a6b0df" + }, { "label": "JBrowse2 Single Haplotype with related species", "output_name": "JBrowse2 Single Haplotype with related species", "uuid": "3c519fbb-453d-418c-8af3-e4532cf23c28" + } + ] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 12, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 2, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "when": { + "id": 9, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1", + "name": "JBrowse2", + "outputs": [ { - "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", - "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", - "uuid": "2dc05ed1-2c39-45a0-b07c-2ec4b8a6b0df" + "name": "output", + "type": "html" + } + ], + "position": { + "left": 1896.5312607039984, + "top": 0.0 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Single Haplotype" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "bda6d01b-ed4d-44b5-9307-4113d25d704c", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype", + "output_name": "output", + "uuid": "20eb67af-6a5e-44f1-a9eb-4cd7c7cf627a" } ] } }, "tags": [], - "uuid": "0569b4db-b204-41dc-b5c9-f5ad1b42265a" + "uuid": "aa94bcea-e6b3-4677-9709-176f6f732c75" }, "tool_id": null, "type": "subworkflow", - "uuid": "7fa40e11-ee9e-4492-852e-fa55278c26fe", + "uuid": "b0c9d1b4-2cfe-46b6-8a59-e2bbf8418997", "when": "$(inputs.when)", "workflow_outputs": [ + { + "label": "JBrowse2 Single Haplotype", + "output_name": "JBrowse2 Single Haplotype", + "uuid": "6a22e395-9c90-4c39-8649-a02200a5f9d3" + }, { "label": "JBrowse2 Single Haplotype with related species", "output_name": "JBrowse2 Single Haplotype with related species", - "uuid": "3a5bf4bd-0e11-4289-b09a-3126d1da9594" + "uuid": "0651be6a-3ad9-4302-a501-702a7d435ea4" }, { "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", - "uuid": "77c9e164-d85b-454e-b996-29fe74100c03" + "uuid": "010b5194-1e89-4f30-9b20-1e3d7eac7aeb" + }, + { + "label": "JBrowse2 Single Haplotype with Gene Track", + "output_name": "JBrowse2 Single Haplotype with Gene Track", + "uuid": "4eacbf80-e972-46c8-afe6-e90d72faa758" } ] }, @@ -1577,22 +1775,22 @@ "id": 19, "input_connections": { "Coverage": { - "id": 11, + "id": 10, "input_subworkflow_step_id": 6, "output_name": "output" }, "Gaps": { - "id": 10, + "id": 9, "input_subworkflow_step_id": 5, "output_name": "output" }, "Genes": { - "id": 16, + "id": 15, "input_subworkflow_step_id": 8, "output_name": "data_param" }, "Genes?": { - "id": 6, + "id": 5, "input_subworkflow_step_id": 7, "output_name": "output" }, @@ -1607,17 +1805,17 @@ "output_name": "data_param" }, "Related Species": { - "id": 15, + "id": 16, "input_subworkflow_step_id": 2, "output_name": "output1" }, "Telomeres P": { - "id": 9, + "id": 8, "input_subworkflow_step_id": 4, "output_name": "output" }, "Telomeres Q": { - "id": 8, + "id": 7, "input_subworkflow_step_id": 3, "output_name": "output" }, @@ -1892,6 +2090,63 @@ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", "errors": null, "id": 9, + "input_connections": { + "query": { + "id": 0, + "output_name": "output" + }, + "reflist": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": "Align Haplotypes Hap1 is query", + "name": "mashmap", + "outputs": [ + { + "name": "mashout", + "type": "paf" + } + ], + "position": { + "left": 1507.3273804321968, + "top": 793.8614046625582 + }, + "post_job_actions": { + "HideDatasetActionmashout": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "mashout" + }, + "RenameDatasetActionmashout": { + "action_arguments": { + "newname": "Alignment Hap1 vs Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "mashout" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a3a6b0b31f2d", + "name": "mashmap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dense\": false, \"filter_mode\": \"map\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"90.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.1.3+galaxy0", + "type": "tool", + "uuid": "c7740c1c-5674-43d4-aa00-aeca2dcc7fa6", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "errors": null, + "id": 10, "input_connections": { "query": { "id": 0, @@ -1944,11 +2199,11 @@ "when": null, "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", "errors": null, - "id": 10, + "id": 11, "input_connections": { "query": { "id": 2, @@ -2001,9 +2256,161 @@ "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", - "id": 11, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 12, + "input_connections": { + "input_param_type|input_param": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 1107.9772160860653, + "top": 1163.288147730554 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": true, \"to\": \"False\"}, {\"__index__\": 1, \"from\": false, \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "03bd04b4-815e-471e-8bf2-b51054b8390e", + "when": null, + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 13, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 9, + "output_name": "mashout" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_1|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_1|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_1|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "output" + }, + "when": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "name": "JBrowse2", + "outputs": [ + { + "name": "output", + "type": "html" + } + ], + "position": { + "left": 2146.8088643141236, + "top": 602.2449366027035 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Hap1 vs Hap2 with gene tracks" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Alignments\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "8579f589-f836-4f8e-ad72-aa14a8b6c450", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "output_name": "output", + "uuid": "4db7f57b-58ba-4932-9d15-8a0e3cde1f9b" + } + ] + }, + "14": { + "annotation": "", + "id": 14, "input_connections": { "Coverage": { "id": 6, @@ -2031,7 +2438,7 @@ "output_name": "output" }, "Hap1 vs Species": { - "id": 9, + "id": 10, "input_subworkflow_step_id": 4, "output_name": "mashout" }, @@ -2046,7 +2453,7 @@ "output_name": "output" }, "Species vs Hap2": { - "id": 10, + "id": 11, "input_subworkflow_step_id": 3, "output_name": "mashout" }, @@ -2066,8 +2473,8 @@ "name": "Jbrowse2 for 1 related species", "outputs": [], "position": { - "left": 2292.870790775461, - "top": 343.7939440488241 + "left": 1887.4863910257557, + "top": 102.53355703483975 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2387,12 +2794,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map parameter value", - "name": "input_param_type" - } - ], + "inputs": [], "label": "No Gene track", "name": "Map parameter value", "outputs": [ @@ -2656,36 +3058,144 @@ "uuid": "e134915a-f5b7-4b32-a511-921e0b363bff", "when": null, "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "uuid": "ca3249af-b46a-450d-8dbe-696490325d42" + }, { "label": "JBrowse2 Hap1 and hap2 with related species", "output_name": "JBrowse2 Hap1 and hap2 with related species", "uuid": "7562c81f-4b86-4932-8056-52f4dc17d2a9" + } + ] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 15, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 9, + "output_name": "mashout" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_1|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_1|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" }, + "when": { + "id": 12, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 vs Hap2", + "name": "JBrowse2", + "outputs": [ { - "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "uuid": "ca3249af-b46a-450d-8dbe-696490325d42" + "name": "output", + "type": "html" + } + ], + "position": { + "left": 2427.3955083914084, + "top": 101.59146846369417 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Hap1 vs Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Alignments\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "1838736c-68a4-41fd-b6c8-cd4de0aad595", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 vs Hap2", + "output_name": "output", + "uuid": "a3d1e37d-ea4d-44e6-ac96-c456fef1395f" } ] } }, "tags": [], - "uuid": "ef9af3c8-a765-4077-9cb2-9ad16d1a570e" + "uuid": "feda97a2-4c3f-4211-80f4-3c4cd83555a0" }, "tool_id": null, "type": "subworkflow", - "uuid": "af188630-081d-489b-b46f-eae324b3df01", + "uuid": "c65e39fb-f036-47f7-9bd1-c63d161b736f", "when": "$(inputs.when)", "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "uuid": "4a390dc0-8929-4bf5-aea4-2ca8352a8987" + }, { "label": "JBrowse2 Hap1 and hap2 with related species", "output_name": "JBrowse2 Hap1 and hap2 with related species", - "uuid": "6861e850-7a02-47cf-aab2-4093019878e9" + "uuid": "1d0f2614-f167-446d-b874-f2435995ca7a" }, { - "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "uuid": "edb52be2-a128-49cb-9c82-e693d7b7656c" + "label": "JBrowse2 Hap1 vs Hap2", + "output_name": "JBrowse2 Hap1 vs Hap2", + "uuid": "a0cefb53-5c71-4e7a-8415-760c5f49d254" + }, + { + "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "output_name": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "uuid": "42a88cd2-d2d5-4cfe-a00c-145d647cb12b" } ] }, @@ -2731,7 +3241,7 @@ "tool_uuid": null, "tool_version": "5.1.0", "type": "tool", - "uuid": "c70c2d41-43fe-4601-a3aa-8ca8a5433c0a", + "uuid": "6e2e1a5d-5849-4852-898d-6646c379ee0d", "when": null, "workflow_outputs": [] }, @@ -2757,7 +3267,7 @@ ], "position": { "left": 2853.562857058991, - "top": 0.0 + "top": 0 }, "post_job_actions": { "ChangeDatatypeActionoutfile": { @@ -2784,7 +3294,7 @@ "tool_uuid": null, "tool_version": "9.5+galaxy3", "type": "tool", - "uuid": "19ffba37-86b9-4fe3-aae8-f8fbfa2d4ff0", + "uuid": "4e7c4704-4734-49f8-b51e-53c500853bbc", "when": null, "workflow_outputs": [] }, @@ -2824,7 +3334,7 @@ "tool_uuid": null, "tool_version": "1.0.0", "type": "tool", - "uuid": "b00153cb-f706-4e4a-bda6-4b3e859858f6", + "uuid": "71d76ee3-7dac-450a-98e9-bb57111df8c5", "when": null, "workflow_outputs": [] }, @@ -2864,7 +3374,7 @@ "tool_uuid": null, "tool_version": "1.0.0", "type": "tool", - "uuid": "b1b48543-f5a6-410b-aeb6-86c058dee9e3", + "uuid": "2da84228-d818-493b-bafd-a95959ee2de3", "when": null, "workflow_outputs": [] }, @@ -2904,7 +3414,7 @@ "tool_uuid": null, "tool_version": "0.1.0", "type": "tool", - "uuid": "0d89e2e9-fec0-4bc8-a3fc-513dc91f2f1b", + "uuid": "c03bb38c-3383-4d3f-843f-9f74c70b1c47", "when": null, "workflow_outputs": [] }, @@ -2944,7 +3454,7 @@ "tool_uuid": null, "tool_version": "0.1.0", "type": "tool", - "uuid": "9f9a8b3d-6d0a-424f-aae0-4db2e0c16940", + "uuid": "5ad8559e-e863-45e9-bae2-ede8be8314c7", "when": null, "workflow_outputs": [] }, @@ -2994,7 +3504,7 @@ "tool_uuid": null, "tool_version": "0.1.0", "type": "tool", - "uuid": "34cce52f-7548-4454-94ad-ee1547b25636", + "uuid": "bdc1a0bf-1614-47f8-90f8-89cc139edf9a", "when": null, "workflow_outputs": [] }, @@ -3009,12 +3519,7 @@ "output_name": "integer_param" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map parameter value", - "name": "input_param_type" - } - ], + "inputs": [], "label": "Fail if there are duplicated sequence names between the fasta files", "name": "Map parameter value", "outputs": [ @@ -3047,19 +3552,19 @@ "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "84eeffe0-4578-4857-8555-841769a58073", + "uuid": "4af8e08f-5777-40db-b483-89d68084369b", "when": null, "workflow_outputs": [ { "label": "Fail if there are duplicated sequence names between the fasta files", "output_name": "output_param_boolean", - "uuid": "b4ebfb36-d369-4ced-964c-450c62e01b7d" + "uuid": "3928e6f8-3d1b-46dc-b5dc-8d5bae43deb7" } ] } }, "tags": [], - "uuid": "2e394d56-6c89-4588-956e-5c1a9abd33c2", - "version": 1, - "release": "0.1" -} \ No newline at end of file + "uuid": "62ed4482-aaa8-4942-b327-e16cae8f537f", + "version": 18, + "readme": "# JBrowse2 Precuration Tracks with Related Species Alignments\n\nThis workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species.\n\nThe workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser.\n\n## Inputs\n\n### Required Inputs\n\n1. **Species Name** [text] - Species identifier used in the assembly info report\n2. **Assembly Name** [text] - Assembly identifier (e.g., toLID)\n3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names)\n4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes)\n6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`).\n7. **Telomere P** [BED] - P-arm telomere coordinates\n8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty)\n9. **Gaps** [BED] - Assembly gap coordinates\n10. **Coverage** [BigWig] - PacBio HiFi read coverage track\n\n### Gene Annotation Options\n\n11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance\n12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled)\n\n## Outputs\n\n1. **Assembly Info** - Summary of species and assembly name\n2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used)\n3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included\n4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used)\n5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Additional outputs\n\nThese JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view.\n\n6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments\n7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included\n8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments\n9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Validation output\n\n10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas.\n\n## Usage Notes\n\n### Pairing with the Hi-C contact map workflow\n\nThis workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow:\n\n| Hi-C workflow output | Use here as input |\n|---|---|\n| `Decontaminated Hap1 with Suffix` | `Haplotype 1` |\n| `Decontaminated Hap2 with Suffix` | `Haplotype 2` |\n| `P telomeres bed` | `Telomere P` |\n| `Q telomeres Bed` | `Telomere Q` |\n| `Gaps Bed` | `Gaps` |\n| `BigWig Coverage` | `Coverage` |\n| `Compleasm Genes track` | `Genes` |\n\n### Related species selection\n\nChoose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection.\n\n**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example:\n\n```bash\nzcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz\n```\n\n### Scaffold name suffixes\n\nIf using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks.\n\n## Citation\n\nIf you use this workflow, please cite:\n- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z))\n- minimap2 (used for related-species alignment)\n- Other tools as listed in the workflow\n" +} diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md index a3251b683a..d0d3cbf613 100644 --- a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md @@ -32,6 +32,19 @@ The workflow takes the assembly haplotype(s) and the precuration tracks (telomer 4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used) 5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included +### Additional outputs + +These JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view. + +6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments +7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included +8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments +9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included + +### Validation output + +10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas. + ## Usage Notes ### Pairing with the Hi-C contact map workflow From f38752ec88dd2ce454f75d7fe71c6fcb4ed08253 Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Wed, 13 May 2026 09:51:33 -0400 Subject: [PATCH 3/3] Simplify and add jbrowse2 instances without related species --- ...ration-Jbrowse-tracks-alignments-tests.yml | 4 - .../Precuration-Jbrowse-tracks-alignments.ga | 4760 +++++++++++------ .../README.md | 56 +- 3 files changed, 3178 insertions(+), 1642 deletions(-) diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml index 6d8f198073..41fcaa7053 100644 --- a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments-tests.yml @@ -17,7 +17,6 @@ hashes: - hash_function: SHA-1 hash_value: a0ee25fd9f7cf223ca40ff530e1201589fade212 - Will you use a second haplotype?: false Related Species: class: Collection collection_type: list @@ -36,7 +35,6 @@ hashes: - hash_function: SHA-1 hash_value: bd70fbde965e16ee88b54223d6dfe67989d3865f - Do you want to provide gene annotation for your assembly?: false Telomere P: class: File location: https://zenodo.org/records/20074725/files/P_telomeres.bed @@ -86,7 +84,6 @@ hashes: - hash_function: SHA-1 hash_value: a0ee25fd9f7cf223ca40ff530e1201589fade212 - Will you use a second haplotype?: true Haplotype 2: class: File location: https://zenodo.org/records/20074725/files/Haplotype_2.fasta @@ -112,7 +109,6 @@ hashes: - hash_function: SHA-1 hash_value: bd70fbde965e16ee88b54223d6dfe67989d3865f - Do you want to provide gene annotation for your assembly?: true Genes: class: File location: https://zenodo.org/records/20074725/files/Compleasm_genes_track.gff diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga index 4d82d0aafe..de168248a1 100644 --- a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/Precuration-Jbrowse-tracks-alignments.ga @@ -39,7 +39,7 @@ "outputs": [], "position": { "left": 0, - "top": 113.32852983289965 + "top": 64.56706309674621 }, "tool_id": null, "tool_state": "{\"multiple\": false, \"validators\": [], \"parameter_type\": \"text\", \"optional\": false}", @@ -66,7 +66,7 @@ "outputs": [], "position": { "left": 95.65671993217956, - "top": 204.52575895443343 + "top": 155.76429221828 }, "tool_id": null, "tool_state": "{\"multiple\": false, \"validators\": [], \"parameter_type\": \"text\", \"optional\": false}", @@ -93,7 +93,7 @@ "outputs": [], "position": { "left": 198.28766556712145, - "top": 333.06630818129815 + "top": 284.3048414451447 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -104,37 +104,10 @@ "workflow_outputs": [] }, "3": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 3, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Will you use a second haplotype?" - } - ], - "label": "Will you use a second haplotype?", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 301.8902333217979, - "top": 405.0410156580133 - }, - "tool_id": null, - "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "1f933849-8bc5-47ff-83da-7f53006c39cf", - "when": null, - "workflow_outputs": [] - }, - "4": { "annotation": "Assembly for Haplotype 2. If \"Will you use a second haplotype?\" is set to \"no\", use haplotype 1 here. ", "content_id": null, "errors": null, - "id": 4, + "id": 3, "input_connections": {}, "inputs": [ { @@ -146,8 +119,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 415.3930839522133, - "top": 539.8438023368923 + "left": 321.8732762998182, + "top": 399.83130302028997 }, "tool_id": null, "tool_state": "{\"optional\": true, \"format\": [\"fasta\"], \"tag\": null}", @@ -157,38 +130,11 @@ "when": null, "workflow_outputs": [] }, - "5": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 5, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Do you want to provide gene annotation for your assembly?" - } - ], - "label": "Do you want to provide gene annotation for your assembly?", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 532.8506745873698, - "top": 662.309181460891 - }, - "tool_id": null, - "tool_state": "{\"default\": false, \"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "ae28b111-3e2f-4506-b653-97b4cebcee72", - "when": null, - "workflow_outputs": [] - }, - "6": { + "4": { "annotation": "", "content_id": null, "errors": null, - "id": 6, + "id": 4, "input_connections": {}, "inputs": [ { @@ -200,8 +146,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 614.6440902431865, - "top": 818.8033806207972 + "left": 460.3563529960522, + "top": 529.5975044587185 }, "tool_id": null, "tool_state": "{\"optional\": true, \"format\": [\"gff3\"], \"tag\": null}", @@ -211,11 +157,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "5": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 5, "input_connections": {}, "inputs": [ { @@ -227,8 +173,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 680.5676592646699, - "top": 901.3563409388138 + "left": 579.1058347276563, + "top": 646.1816269398256 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", @@ -238,11 +184,11 @@ "when": null, "workflow_outputs": [] }, - "8": { + "6": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 6, "input_connections": {}, "inputs": [ { @@ -254,8 +200,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 761.1770988870501, - "top": 998.8551768278469 + "left": 671.0474417062338, + "top": 757.1049343640235 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", @@ -265,11 +211,11 @@ "when": null, "workflow_outputs": [] }, - "9": { + "7": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 7, "input_connections": {}, "inputs": [ { @@ -281,8 +227,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 816.7956506700089, - "top": 1085.617189755827 + "left": 774.9938551754473, + "top": 870.9665747424492 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", @@ -292,11 +238,11 @@ "when": null, "workflow_outputs": [] }, - "10": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 10, + "id": 8, "input_connections": {}, "inputs": [ { @@ -308,8 +254,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 889.9015443268538, - "top": 1165.3201006570696 + "left": 849.5535664328285, + "top": 975.6679392124566 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": null}", @@ -319,11 +265,11 @@ "when": null, "workflow_outputs": [] }, - "11": { + "9": { "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", "content_id": null, "errors": null, - "id": 11, + "id": 9, "input_connections": {}, "inputs": [ { @@ -335,22 +281,22 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 1016.2648364611407, - "top": 1255.890937169875 + "left": 951.676946611419, + "top": 1071.3522608342273 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_state": "{\"optional\": true, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", "tool_version": null, "type": "data_collection_input", "uuid": "b1d57707-483c-43cd-8256-0a2888af1246", "when": null, "workflow_outputs": [] }, - "12": { + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 12, + "id": 10, "input_connections": { "components_0|param_type|component_value": { "id": 0, @@ -371,8 +317,8 @@ } ], "position": { - "left": 1513.3687877339703, - "top": 196.67349674870826 + "left": 1494.2245235926566, + "top": 0 }, "post_job_actions": { "HideDatasetActionout1": { @@ -409,11 +355,11 @@ } ] }, - "13": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 13, + "id": 11, "input_connections": { "input_param_type|input_param": { "id": 3, @@ -421,7 +367,7 @@ } }, "inputs": [], - "label": "Only one Haplotype", + "label": "Two Haplotypes", "name": "Map parameter value", "outputs": [ { @@ -430,8 +376,8 @@ } ], "position": { - "left": 1736.3581103638398, - "top": 455.0639514218991 + "left": 1253.1907400797504, + "top": 628.6659493845017 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -447,22 +393,22 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": true, \"to\": \"False\"}, {\"__index__\": 1, \"from\": false, \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "df19ed91-a001-4caa-91f8-8d9051fde5c9", + "uuid": "4b9805d1-c6d8-4b9d-85a4-d80c93925869", "when": null, "workflow_outputs": [] }, - "14": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 14, + "id": 12, "input_connections": { "style_cond|type_cond|pick_from_0|value": { - "id": 4, + "id": 3, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { @@ -481,7 +427,7 @@ ], "position": { "left": 1706.8744833487017, - "top": 654.7944887566696 + "top": 606.0330220205161 }, "post_job_actions": { "HideDatasetActiondata_param": { @@ -505,522 +451,1114 @@ "when": null, "workflow_outputs": [] }, - "15": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", - "errors": null, - "id": 15, - "input_connections": { - "style_cond|type_cond|pick_from_0|value": { - "id": 6, - "output_name": "output" - }, - "style_cond|type_cond|pick_from_1|value": { - "id": 9, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Pick parameter value", - "outputs": [ - { - "name": "data_param", - "type": "input" - } - ], - "position": { - "left": 2050.977397800029, - "top": 1042.9931586846508 - }, - "post_job_actions": { - "HideDatasetActiondata_param": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "data_param" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", - "tool_shed_repository": { - "changeset_revision": "b19e21af9c52", - "name": "pick_value", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "0.2.0", - "type": "tool", - "uuid": "87a497ce-176b-4e85-adf2-0f3e58b24670", - "when": null, - "workflow_outputs": [] - }, - "16": { - "annotation": "", - "content_id": "CONVERTER_gz_to_uncompressed", - "errors": null, - "id": 16, - "input_connections": { - "input1": { - "id": 11, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Convert gz compressed file to uncompressed.", - "outputs": [ - { - "name": "output1", - "type": "auto" - } - ], - "position": { - "left": 1685.3438207068607, - "top": 928.4985122876616 - }, - "post_job_actions": { - "ChangeDatatypeActionoutput1": { - "action_arguments": { - "newtype": "fasta" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "output1" - }, - "HideDatasetActionoutput1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output1" - } - }, - "tool_id": "CONVERTER_gz_to_uncompressed", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "1.0.0", - "type": "tool", - "uuid": "6f868700-ff9c-4415-98d7-81befe9dde9e", - "when": null, - "workflow_outputs": [] - }, - "17": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", - "errors": null, - "id": 17, - "input_connections": { - "infile": { - "id": 16, - "output_name": "output1" - } - }, - "inputs": [], - "label": null, - "name": "Search in textfiles", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 2193.787159776598, - "top": 516.9501479775356 - }, - "post_job_actions": { - "ChangeDatatypeActionoutput": { - "action_arguments": { - "newtype": "tabular" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "output" - }, - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", - "tool_shed_repository": { - "changeset_revision": "ab83aa685821", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \">\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "9.5+galaxy3", - "type": "tool", - "uuid": "24671126-d835-4ecf-94c6-f22fa01d6abd", - "when": null, - "workflow_outputs": [] - }, - "18": { + "13": { "annotation": "", - "id": 18, + "id": 13, "input_connections": { - "Coverage": { - "id": 10, - "input_subworkflow_step_id": 5, - "output_name": "output" - }, - "Gaps": { + "Related Species": { "id": 9, - "input_subworkflow_step_id": 4, - "output_name": "output" - }, - "Genes": { - "id": 15, - "input_subworkflow_step_id": 6, - "output_name": "data_param" - }, - "Genes?": { - "id": 5, - "input_subworkflow_step_id": 7, - "output_name": "output" - }, - "Hap1 fasta": { - "id": 2, "input_subworkflow_step_id": 0, "output_name": "output" - }, - "Related Species": { - "id": 16, - "input_subworkflow_step_id": 1, - "output_name": "output1" - }, - "Telomeres P": { - "id": 8, - "input_subworkflow_step_id": 3, - "output_name": "output" - }, - "Telomeres Q": { - "id": 7, - "input_subworkflow_step_id": 2, - "output_name": "output" - }, - "when": { - "id": 13, - "output_name": "output_param_boolean" } }, "inputs": [], "label": null, - "name": "Jbrowse for pre-curation single haplotype - 1 related Species ", + "name": "Map Collection to boolean", "outputs": [], "position": { - "left": 2934.6624331027892, - "top": 744.4198856816727 + "left": 2657.8767092560806, + "top": 53.28010686264924 }, "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6228-2785", + "name": "Patrik Smeds" + }, + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6421-3484", + "name": "Delphine Lariviere" + } + ], "format-version": "0.1", - "name": "Jbrowse for pre-curation single haplotype - 1 related Species ", + "license": "MIT", + "name": "Map Collection to boolean", + "readme": "# JBrowse2 Precuration Tracks with Related Species Alignments\n\nThis workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species.\n\nThe workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser.\n\n## Inputs\n\n### Required Inputs\n\n1. **Species Name** [text] - Species identifier used in the assembly info report\n2. **Assembly Name** [text] - Assembly identifier (e.g., toLID)\n3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names)\n4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes)\n6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`).\n7. **Telomere P** [BED] - P-arm telomere coordinates\n8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty)\n9. **Gaps** [BED] - Assembly gap coordinates\n10. **Coverage** [BigWig] - PacBio HiFi read coverage track\n\n### Gene Annotation Options\n\n11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance\n12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled)\n\n## Outputs\n\n1. **Assembly Info** - Summary of species and assembly name\n2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used)\n3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included\n4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used)\n5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Additional outputs\n\nThese JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view.\n\n6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments\n7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included\n8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments\n9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Validation output\n\n10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas.\n\n## Usage Notes\n\n### Pairing with the Hi-C contact map workflow\n\nThis workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow:\n\n| Hi-C workflow output | Use here as input |\n|---|---|\n| `Decontaminated Hap1 with Suffix` | `Haplotype 1` |\n| `Decontaminated Hap2 with Suffix` | `Haplotype 2` |\n| `P telomeres bed` | `Telomere P` |\n| `Q telomeres Bed` | `Telomere Q` |\n| `Gaps Bed` | `Gaps` |\n| `BigWig Coverage` | `Coverage` |\n| `Compleasm Genes track` | `Genes` |\n\n### Related species selection\n\nChoose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection.\n\n**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example:\n\n```bash\nzcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz\n```\n\n### Scaffold name suffixes\n\nIf using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks.\n\n## Citation\n\nIf you use this workflow, please cite:\n- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z))\n- minimap2 (used for related-species alignment)\n- Other tools as listed in the workflow\n", "report": { - "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + "markdown": "# Precuration workflow on:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Info\")\n```\n\n## Duplication Stats\n\nSamtools markdup deduplication stats (if applicable)\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats\")\n```\n\n\n\nPairtools stats\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats: MultiQC\")\n```\n\n## Telomere report\n\n```galaxy\nhistory_dataset_embedded(output=\"Telomere Report\")\n```\n\n## Pretext Snapshots\n\nWith Multimapping\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks - Multimapping\")\n```\n\n\nWith MAPQ filtering\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks\")\n```\n\n\n" }, "steps": { "0": { - "annotation": "", + "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "", - "name": "Hap1 fasta" + "description": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "name": "Related Species" } ], - "label": "Hap1 fasta", - "name": "Input dataset", + "label": "Related Species", + "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 699.2443289019618 + "top": 0 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_state": "{\"optional\": true, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", "tool_version": null, - "type": "data_input", - "uuid": "4a20362f-2551-4a60-9118-e4c3e7c4f264", + "type": "data_collection_input", + "uuid": "b1d57707-483c-43cd-8256-0a2888af1246", "when": null, "workflow_outputs": [] }, "1": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, "id": 1, - "input_connections": {}, - "inputs": [ + "input_connections": { + "input_param_type|input_param": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": "Two Haplotypes 2", + "name": "Map parameter value", + "outputs": [ { - "description": "", - "name": "Related Species" + "name": "output_param_boolean", + "type": "expression.json" } ], - "label": "Related Species", - "name": "Input dataset collection", - "outputs": [], "position": { - "left": 77.86825459522053, - "top": 794.9152357793989 + "left": 507.52614703835707, + "top": 68.65082494054082 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", - "tool_version": null, - "type": "data_collection_input", - "uuid": "771229b7-cdcc-462a-a1e5-314204a3fca1", + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "30ef2c07-c458-4a90-94b7-5e5ae4885844", "when": null, "workflow_outputs": [] }, "2": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Telomeres Q" + "input_connections": { + "input_param_type|input_param": { + "id": 1, + "output_name": "output_param_boolean" } - ], - "label": "Telomeres Q", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 162.91806250869854, - "top": 925.5453930768067 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", - "when": null, - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 3, - "input_connections": {}, - "inputs": [ + "inputs": [], + "label": "Two Haplotypes 3", + "name": "Map parameter value", + "outputs": [ { - "description": "", - "name": "Telomeres P" + "name": "output_param_text", + "type": "expression.json" } ], - "label": "Telomeres P", - "name": "Input dataset", - "outputs": [], "position": { - "left": 235.76054218223504, - "top": 1049.1809061513864 + "left": 801.9711946226973, + "top": 268.066568476228 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", - "when": null, - "workflow_outputs": [] - }, - "4": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 4, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Gaps" + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + }, + "HideDatasetActionoutput_param_text": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_text" } - ], - "label": "Gaps", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 325.8334374647798, - "top": 1143.422158149443 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "5be371df-1c67-42ae-a535-da4ca4bf1e51", "when": null, "workflow_outputs": [] }, - "5": { + "3": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3", "errors": null, - "id": 5, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Coverage" + "id": 3, + "input_connections": { + "token_set_0|line": { + "id": 2, + "output_name": "output_param_text" } - ], - "label": "Coverage", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 426.80614784345863, - "top": 1246.4956813108688 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "738f43fc-5f88-4117-bcc3-4a9c1b01c0a1", - "when": null, - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 6, - "input_connections": {}, - "inputs": [ + "inputs": [], + "label": null, + "name": "Create text file", + "outputs": [ { - "description": "", - "name": "Genes" + "name": "outfile", + "type": "txt" } ], - "label": "Genes", - "name": "Input dataset", - "outputs": [], "position": { - "left": 481.54024694955143, - "top": 1345.5356433169977 + "left": 1031.2529071684971, + "top": 141.25993418553026 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "3831fc6f-0526-46ab-869b-5a07c6cded67", - "when": null, - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 7, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Genes?" + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" } - ], - "label": "Genes?", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 535.8872921148474, - "top": 1451.6354804278585 }, - "tool_id": null, - "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "bc1b0c8a-64af-4cac-a825-6eb7a70cbbeb", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": {\"__class__\": \"ConnectedValue\"}, \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "f2c6b8fd-f348-494d-867e-28d82492a589", "when": null, "workflow_outputs": [] }, - "8": { + "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3", "errors": null, - "id": 8, + "id": 4, "input_connections": { - "query": { - "id": 0, - "output_name": "output" - }, - "reflist": { - "id": 1, - "output_name": "output" + "inputs": { + "id": 3, + "output_name": "outfile" } }, "inputs": [], - "label": "hap1 vs species", - "name": "mashmap", + "label": null, + "name": "Concatenate datasets", "outputs": [ { - "name": "mashout", - "type": "paf" + "name": "out_file1", + "type": "input" } ], "position": { - "left": 1026.595772250997, - "top": 858.7635819182626 + "left": 1404.1850282401706, + "top": 159.59233303291586 }, "post_job_actions": { - "HideDatasetActionmashout": { + "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "mashout" - }, - "RenameDatasetActionmashout": { - "action_arguments": { - "newname": "hap1 vs species" - }, - "action_type": "RenameDatasetAction", - "output_name": "mashout" + "output_name": "out_file1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "a3a6b0b31f2d", - "name": "mashmap", - "owner": "iuc", + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"85.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "3.1.3+galaxy0", + "tool_version": "9.5+galaxy3", "type": "tool", - "uuid": "b1a857dd-1140-4641-943b-cb141b6a6f81", + "uuid": "951df8ae-cb04-448c-9b26-1b1c72e52354", "when": null, "workflow_outputs": [] }, - "9": { + "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "content_id": "Show beginning1", "errors": null, - "id": 9, + "id": 5, "input_connections": { - "input_param_type|input_param": { - "id": 7, - "output_name": "output" + "input": { + "id": 4, + "output_name": "out_file1" } }, "inputs": [], "label": null, - "name": "Map parameter value", + "name": "Select first", "outputs": [ { - "name": "output_param_boolean", - "type": "expression.json" + "name": "out_file1", + "type": "input" } ], "position": { - "left": 909.3164880438957, - "top": 1632.3549251437048 + "left": 1591.5813587970113, + "top": 415.32944461901855 }, "post_job_actions": { - "HideDatasetActionoutput_param_boolean": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Show beginning1", + "tool_state": "{\"header\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineNum\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.2", + "type": "tool", + "uuid": "6777b035-d40f-471e-b677-c886520c5f08", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 6, + "input_connections": { + "input1": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "boolean_param", + "type": "expression.json" + } + ], + "position": { + "left": 1900.9513665053723, + "top": 426.5056982072265 + }, + "post_job_actions": {}, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"boolean\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "39916b95-3287-497f-83ea-822bb970a388", + "when": null, + "workflow_outputs": [ + { + "label": "boolean_param", + "output_name": "boolean_param", + "uuid": "651aac03-f463-4bb0-bae9-c1e6d0d808d8" + } + ] + } + }, + "tags": [], + "uuid": "877369eb-5f6e-4a0f-9519-c6f3bb328653" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "8669739f-1749-4124-8391-0bcaf518a2ba", + "when": null, + "workflow_outputs": [] + }, + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 14, + "input_connections": { + "input_param_type|input_param": { + "id": 11, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "Only one Haplotype", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 1736.3581103638398, + "top": 406.30248468574564 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": true, \"to\": \"False\"}, {\"__index__\": 1, \"from\": false, \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "df19ed91-a001-4caa-91f8-8d9051fde5c9", + "when": null, + "workflow_outputs": [] + }, + "15": { + "annotation": "", + "id": 15, + "input_connections": { + "Coverage": { + "id": 8, + "input_subworkflow_step_id": 6, + "output_name": "output" + }, + "Gaps": { + "id": 7, + "input_subworkflow_step_id": 5, + "output_name": "output" + }, + "Genes": { + "id": 4, + "input_subworkflow_step_id": 7, + "output_name": "output" + }, + "Hap1 fasta": { + "id": 2, + "input_subworkflow_step_id": 0, + "output_name": "output" + }, + "Hap2 fasta": { + "id": 12, + "input_subworkflow_step_id": 1, + "output_name": "data_param" + }, + "Related Species": { + "id": 9, + "input_subworkflow_step_id": 2, + "output_name": "output" + }, + "Telomeres P": { + "id": 6, + "input_subworkflow_step_id": 4, + "output_name": "output" + }, + "Telomeres Q": { + "id": 5, + "input_subworkflow_step_id": 3, + "output_name": "output" + }, + "when": { + "id": 11, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": null, + "name": "Jbrowse for pre-curation", + "outputs": [], + "position": { + "left": 3359.99060088773, + "top": 733.3009897445525 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "format-version": "0.1", + "name": "Jbrowse for pre-curation", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 fasta" + } + ], + "label": "Hap1 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 0, + "top": 89.79666666028459 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "4a20362f-2551-4a60-9118-e4c3e7c4f264", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap2 fasta" + } + ], + "label": "Hap2 fasta", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 51.81545453466647, + "top": 209.29539228726594 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "177f6825-e58e-45e9-a3fc-8c7623187e02", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 249.05479741897238, + "top": 610.6761230025993 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "20f7abfb-20b8-49bb-b522-cd911fd1ec4c", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres Q" + } + ], + "label": "Telomeres Q", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 347.4491076529599, + "top": 770.2540634659473 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Telomeres P" + } + ], + "label": "Telomeres P", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 455.5329585464028, + "top": 874.3517570740245 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gaps" + } + ], + "label": "Gaps", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 524.1536909971493, + "top": 967.7185159530706 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Coverage" + } + ], + "label": "Coverage", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 581.1909253334677, + "top": 1054.8379828664645 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "738f43fc-5f88-4117-bcc3-4a9c1b01c0a1", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes" + } + ], + "label": "Genes", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 683.9939626471161, + "top": 1247.6492139360419 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "dabdef6f-cb85-410c-a5ef-229d9ae21a3b", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "errors": null, + "id": 8, + "input_connections": { + "query": { + "id": 0, + "output_name": "output" + }, + "reflist": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": "Align Haplotypes Hap1 is query", + "name": "mashmap", + "outputs": [ + { + "name": "mashout", + "type": "paf" + } + ], + "position": { + "left": 1618.8488760964965, + "top": 794.9612701920845 + }, + "post_job_actions": { + "HideDatasetActionmashout": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "mashout" + }, + "RenameDatasetActionmashout": { + "action_arguments": { + "newname": "Alignment Hap1 vs Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "mashout" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a3a6b0b31f2d", + "name": "mashmap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dense\": false, \"filter_mode\": \"map\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"90.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.1.3+galaxy0", + "type": "tool", + "uuid": "c7740c1c-5674-43d4-aa00-aeca2dcc7fa6", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "id": 9, + "input_connections": { + "Related Species": { + "id": 2, + "input_subworkflow_step_id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map Collection to boolean", + "outputs": [], + "position": { + "left": 746.0912271164992, + "top": 99.3825085692532 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6228-2785", + "name": "Patrik Smeds" + }, + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6421-3484", + "name": "Delphine Lariviere" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "Map Collection to boolean", + "readme": "# JBrowse2 Precuration Tracks with Related Species Alignments\n\nThis workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species.\n\nThe workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser.\n\n## Inputs\n\n### Required Inputs\n\n1. **Species Name** [text] - Species identifier used in the assembly info report\n2. **Assembly Name** [text] - Assembly identifier (e.g., toLID)\n3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names)\n4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes)\n6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`).\n7. **Telomere P** [BED] - P-arm telomere coordinates\n8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty)\n9. **Gaps** [BED] - Assembly gap coordinates\n10. **Coverage** [BigWig] - PacBio HiFi read coverage track\n\n### Gene Annotation Options\n\n11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance\n12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled)\n\n## Outputs\n\n1. **Assembly Info** - Summary of species and assembly name\n2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used)\n3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included\n4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used)\n5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Additional outputs\n\nThese JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view.\n\n6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments\n7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included\n8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments\n9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Validation output\n\n10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas.\n\n## Usage Notes\n\n### Pairing with the Hi-C contact map workflow\n\nThis workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow:\n\n| Hi-C workflow output | Use here as input |\n|---|---|\n| `Decontaminated Hap1 with Suffix` | `Haplotype 1` |\n| `Decontaminated Hap2 with Suffix` | `Haplotype 2` |\n| `P telomeres bed` | `Telomere P` |\n| `Q telomeres Bed` | `Telomere Q` |\n| `Gaps Bed` | `Gaps` |\n| `BigWig Coverage` | `Coverage` |\n| `Compleasm Genes track` | `Genes` |\n\n### Related species selection\n\nChoose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection.\n\n**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example:\n\n```bash\nzcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz\n```\n\n### Scaffold name suffixes\n\nIf using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks.\n\n## Citation\n\nIf you use this workflow, please cite:\n- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z))\n- minimap2 (used for related-species alignment)\n- Other tools as listed in the workflow\n", + "report": { + "markdown": "# Precuration workflow on:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Info\")\n```\n\n## Duplication Stats\n\nSamtools markdup deduplication stats (if applicable)\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats\")\n```\n\n\n\nPairtools stats\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats: MultiQC\")\n```\n\n## Telomere report\n\n```galaxy\nhistory_dataset_embedded(output=\"Telomere Report\")\n```\n\n## Pretext Snapshots\n\nWith Multimapping\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks - Multimapping\")\n```\n\n\nWith MAPQ filtering\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks\")\n```\n\n\n" + }, + "steps": { + "0": { + "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 0, + "top": 0 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "b1d57707-483c-43cd-8256-0a2888af1246", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 1, + "input_connections": { + "input_param_type|input_param": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": "Two Haplotypes 2", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 507.52614703835707, + "top": 68.65082494054082 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "30ef2c07-c458-4a90-94b7-5e5ae4885844", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 2, + "input_connections": { + "input_param_type|input_param": { + "id": 1, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "Two Haplotypes 3", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_text", + "type": "expression.json" + } + ], + "position": { + "left": 801.9711946226973, + "top": 268.066568476228 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + }, + "HideDatasetActionoutput_param_text": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_text" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "5be371df-1c67-42ae-a535-da4ca4bf1e51", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3", + "errors": null, + "id": 3, + "input_connections": { + "token_set_0|line": { + "id": 2, + "output_name": "output_param_text" + } + }, + "inputs": [], + "label": null, + "name": "Create text file", + "outputs": [ + { + "name": "outfile", + "type": "txt" + } + ], + "position": { + "left": 1031.2529071684971, + "top": 141.25993418553026 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": {\"__class__\": \"ConnectedValue\"}, \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "f2c6b8fd-f348-494d-867e-28d82492a589", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3", + "errors": null, + "id": 4, + "input_connections": { + "inputs": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1404.1850282401706, + "top": 159.59233303291586 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "951df8ae-cb04-448c-9b26-1b1c72e52354", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "Show beginning1", + "errors": null, + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Select first", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1591.5813587970113, + "top": 415.32944461901855 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Show beginning1", + "tool_state": "{\"header\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineNum\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.2", + "type": "tool", + "uuid": "6777b035-d40f-471e-b677-c886520c5f08", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 6, + "input_connections": { + "input1": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "boolean_param", + "type": "expression.json" + } + ], + "position": { + "left": 1900.9513665053723, + "top": 426.5056982072265 + }, + "post_job_actions": {}, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"boolean\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "39916b95-3287-497f-83ea-822bb970a388", + "when": null, + "workflow_outputs": [ + { + "label": "boolean_param", + "output_name": "boolean_param", + "uuid": "651aac03-f463-4bb0-bae9-c1e6d0d808d8" + } + ] + } + }, + "tags": [], + "uuid": "877369eb-5f6e-4a0f-9519-c6f3bb328653" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "1e7bc4d3-c4e5-42df-bf18-beb340b1493b", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 10, + "input_connections": { + "input_param_type|input_param": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 1187.515644704917, + "top": 1370.7082691223843 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_param_boolean" @@ -1033,33 +1571,201 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": true, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "a8eddf6e-6019-46b9-bda4-3cae4f66baf1", + "uuid": "627f5baa-1be8-4c50-8708-88ce7c0c86c3", "when": null, "workflow_outputs": [] }, - "10": { + "11": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "errors": null, + "id": 11, + "input_connections": { + "query": { + "id": 0, + "output_name": "output" + }, + "reflist": { + "id": 2, + "output_name": "output" + }, + "when": { + "id": 9, + "output_name": "boolean_param" + } + }, + "inputs": [], + "label": "Hap1 vs Species", + "name": "mashmap", + "outputs": [ + { + "name": "mashout", + "type": "paf" + } + ], + "position": { + "left": 1373.796550800666, + "top": 190.60802095876576 + }, + "post_job_actions": { + "HideDatasetActionmashout": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "mashout" + }, + "RenameDatasetActionmashout": { + "action_arguments": { + "newname": "Species to Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "mashout" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a3a6b0b31f2d", + "name": "mashmap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"85.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.1.3+galaxy0", + "type": "tool", + "uuid": "ba8fe065-a989-4cff-bcda-2e6883b1f6cd", + "when": "$(inputs.when)", + "workflow_outputs": [] + }, + "12": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "errors": null, + "id": 12, + "input_connections": { + "query": { + "id": 2, + "output_name": "output" + }, + "reflist": { + "id": 1, + "output_name": "output" + }, + "when": { + "id": 9, + "output_name": "boolean_param" + } + }, + "inputs": [], + "label": "Species vs Hap2", + "name": "mashmap", + "outputs": [ + { + "name": "mashout", + "type": "paf" + } + ], + "position": { + "left": 1373.0046279283763, + "top": 474.33892908289124 + }, + "post_job_actions": { + "HideDatasetActionmashout": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "mashout" + }, + "RenameDatasetActionmashout": { + "action_arguments": { + "newname": "Species to Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "mashout" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_shed_repository": { + "changeset_revision": "a3a6b0b31f2d", + "name": "mashmap", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"85.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.1.3+galaxy0", + "type": "tool", + "uuid": "cf1e95b5-3bd6-41c1-a2d4-93ac6c1b1b1a", + "when": "$(inputs.when)", + "workflow_outputs": [] + }, + "13": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 13, + "input_connections": { + "input_param_type|input_param": { + "id": 10, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": null, + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 1454.7038382847572, + "top": 1062.9892225005478 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": true, \"to\": \"False\"}, {\"__index__\": 1, \"from\": false, \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "03bd04b4-815e-471e-8bf2-b51054b8390e", + "when": null, + "workflow_outputs": [] + }, + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", "errors": null, - "id": 10, + "id": 14, "input_connections": { "assemblies_0|reference_genome|genome": { "id": 0, "output_name": "output" }, "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 2, - "output_name": "output" + "id": 8, + "output_name": "mashout" }, - "assemblies_0|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { "id": 3, "output_name": "output" }, - "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { "id": 4, "output_name": "output" }, @@ -1071,13 +1777,41 @@ "id": 6, "output_name": "output" }, - "when": { + "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_1|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_1|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_1|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { "id": 7, "output_name": "output" + }, + "when": { + "id": 10, + "output_name": "output_param_boolean" } }, "inputs": [], - "label": "JBrowse2 Hap1 with gene track", + "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", "name": "JBrowse2", "outputs": [ { @@ -1086,13 +1820,13 @@ } ], "position": { - "left": 1896.9114798587966, - "top": 990.3320527378663 + "left": 2132.3926171121566, + "top": 631.5194878176554 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "JBrowse2 Single Haplotype with Gene Track" + "newname": "JBrowse2 Hap1 vs Hap2 with gene tracks" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -1105,42 +1839,37 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Alignments\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "3.7.0+galaxy0", "type": "tool", - "uuid": "8244bcfd-113f-4a5f-8b7a-4ebf39a2fd0d", + "uuid": "8579f589-f836-4f8e-ad72-aa14a8b6c450", "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Single Haplotype with Gene Track", + "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", "output_name": "output", - "uuid": "b4b0f191-314c-4519-8ea9-6885a3c3a1e5" + "uuid": "4db7f57b-58ba-4932-9d15-8a0e3cde1f9b" } ] }, - "11": { + "15": { "annotation": "", - "id": 11, + "id": 15, "input_connections": { "Coverage": { - "id": 5, - "input_subworkflow_step_id": 6, + "id": 6, + "input_subworkflow_step_id": 8, "output_name": "output" }, "Gaps": { - "id": 4, - "input_subworkflow_step_id": 5, - "output_name": "output" - }, - "Gene Tracks": { - "id": 6, + "id": 5, "input_subworkflow_step_id": 7, "output_name": "output" }, - "Genes?": { + "Genes": { "id": 7, - "input_subworkflow_step_id": 8, + "input_subworkflow_step_id": 9, "output_name": "output" }, "Hap1 fasta": { @@ -1149,40 +1878,54 @@ "output_name": "output" }, "Hap1 vs Species": { - "id": 8, - "input_subworkflow_step_id": 2, + "id": 11, + "input_subworkflow_step_id": 4, "output_name": "mashout" }, - "Related Fasta": { + "Hap2 fasta": { "id": 1, "input_subworkflow_step_id": 1, "output_name": "output" }, + "Related Species": { + "id": 2, + "input_subworkflow_step_id": 2, + "output_name": "output" + }, + "Species vs Hap2": { + "id": 12, + "input_subworkflow_step_id": 3, + "output_name": "mashout" + }, "Telomeres P": { - "id": 3, - "input_subworkflow_step_id": 4, + "id": 4, + "input_subworkflow_step_id": 6, "output_name": "output" }, "Telomeres Q": { - "id": 2, - "input_subworkflow_step_id": 3, + "id": 3, + "input_subworkflow_step_id": 5, "output_name": "output" + }, + "when": { + "id": 9, + "output_name": "boolean_param" } }, "inputs": [], "label": null, - "name": "Jbrowse2 for 1 related species - single haplotype", + "name": "Jbrowse2 for 1 related species", "outputs": [], "position": { - "left": 1504.531864079652, - "top": 1218.259001224898 + "left": 1906.299975360162, + "top": 0.0 }, "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", "comments": [], "format-version": "0.1", - "name": "Jbrowse2 for 1 related species - single haplotype", + "name": "Jbrowse2 for 1 related species", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -1204,7 +1947,7 @@ "outputs": [], "position": { "left": 0, - "top": 209.22223652047438 + "top": 271.13908772215916 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -1223,21 +1966,21 @@ "inputs": [ { "description": "", - "name": "Related Fasta" + "name": "Hap2 fasta" } ], - "label": "Related Fasta", + "label": "Hap2 fasta", "name": "Input dataset", "outputs": [], "position": { - "left": 64.19044612855507, - "top": 339.63559170456904 + "left": 53.14881800970572, + "top": 420.7641795440555 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "385825a9-198e-425f-9fb3-55af892d20dc", + "uuid": "177f6825-e58e-45e9-a3fc-8c7623187e02", "when": null, "workflow_outputs": [] }, @@ -1250,21 +1993,21 @@ "inputs": [ { "description": "", - "name": "Hap1 vs Species" + "name": "Related Species" } ], - "label": "Hap1 vs Species", + "label": "Related Species", "name": "Input dataset", "outputs": [], "position": { - "left": 113.31939864522589, - "top": 479.1639618101156 + "left": 98.91709918730632, + "top": 553.1054764799819 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"paf\"], \"tag\": null}", + "tool_state": "{\"optional\": true, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "c18b3a25-89e8-4853-81fe-affb519a9ae0", + "uuid": "604a6bec-8c1f-47e3-8884-c32f63246589", "when": null, "workflow_outputs": [] }, @@ -1274,6 +2017,60 @@ "errors": null, "id": 3, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Species vs Hap2" + } + ], + "label": "Species vs Hap2", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 147.9198303415696, + "top": 670.2931389328182 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"paf\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "ebdc47b3-16f5-48e9-a101-c82b2370181a", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Hap1 vs Species" + } + ], + "label": "Hap1 vs Species", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 175.64670268098203, + "top": 777.2105888619357 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"paf\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "385825a9-198e-425f-9fb3-55af892d20dc", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, "inputs": [ { "description": "", @@ -1284,8 +2081,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 173.91872965677103, - "top": 640.6573469993632 + "left": 206.21568172170709, + "top": 895.0983900914266 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", @@ -1295,11 +2092,11 @@ "when": null, "workflow_outputs": [] }, - "4": { + "6": { "annotation": "", "content_id": null, "errors": null, - "id": 4, + "id": 6, "input_connections": {}, "inputs": [ { @@ -1311,138 +2108,342 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 262.08020244071406, - "top": 799.4536221643712 + "left": 300.9375, + "top": 1049.75 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 7, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gaps" + } + ], + "label": "Gaps", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 353.8919295731858, + "top": 1244.9653893778952 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 8, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Coverage" + } + ], + "label": "Coverage", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 391.49614814580605, + "top": 1410.3962329181184 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", + "tool_version": null, + "type": "data_input", + "uuid": "2131fd1e-4f34-4662-be5c-382101fcbc76", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 9, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Genes" + } + ], + "label": "Genes", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 467.99484572288014, + "top": 1557.4724288450213 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "496c7358-def1-4256-b4e8-6698cac34f97", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 10, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "data_param", + "type": "input" + } + ], + "position": { + "left": 819.3045693419575, + "top": 344.4531003778494 + }, + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_error\", \"__current_case__\": 2, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"RuntimeValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "7399e65c-fc45-48bc-9a66-32ce47c70e9d", "when": null, "workflow_outputs": [] }, - "5": { + "11": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 5, - "input_connections": {}, - "inputs": [ + "id": 11, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ { - "description": "", - "name": "Gaps" + "name": "data_param", + "type": "input" } ], - "label": "Gaps", - "name": "Input dataset", - "outputs": [], "position": { - "left": 334.3294215467986, - "top": 926.268574398666 + "left": 982.8012108841962, + "top": 480.8711270227511 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_error\", \"__current_case__\": 2, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"RuntimeValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "f3d385a7-8a88-459e-8d4b-c680e7a433e7", "when": null, "workflow_outputs": [] }, - "6": { + "12": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 6, - "input_connections": {}, - "inputs": [ + "id": 12, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 4, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ { - "description": "", - "name": "Coverage" + "name": "data_param", + "type": "input" } ], - "label": "Coverage", - "name": "Input dataset", - "outputs": [], "position": { - "left": 431.83941564925703, - "top": 1078.7178133506623 + "left": 908.8858060336889, + "top": 822.840387531385 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "2131fd1e-4f34-4662-be5c-382101fcbc76", + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_error\", \"__current_case__\": 2, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"RuntimeValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "38659345-a8cc-462a-bf02-e7e8ef9a3e80", "when": null, "workflow_outputs": [] }, - "7": { + "13": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 7, - "input_connections": {}, - "inputs": [ + "id": 13, + "input_connections": { + "input_param_type|input_param": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map parameter value", + "outputs": [ { - "description": "", - "name": "Gene Tracks" + "name": "output_param_boolean", + "type": "expression.json" } ], - "label": "Gene Tracks", - "name": "Input dataset", - "outputs": [], "position": { - "left": 564.2214660523151, - "top": 1297.0956580243692 + "left": 894.3942403582007, + "top": 1144.0865983396454 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "f6db855c-e1de-49f7-836c-87a510e955aa", + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "70c8e882-f5c7-42a7-b7a1-db1e27761813", "when": null, "workflow_outputs": [] }, - "8": { + "14": { "annotation": "", - "content_id": null, + "content_id": "CONVERTER_gz_to_uncompressed", "errors": null, - "id": 8, - "input_connections": {}, - "inputs": [ + "id": 14, + "input_connections": { + "input1": { + "id": 10, + "output_name": "data_param" + } + }, + "inputs": [], + "label": null, + "name": "Convert gz compressed file to uncompressed.", + "outputs": [ { - "description": "", - "name": "Genes?" + "name": "output1", + "type": "auto" } ], - "label": "Genes?", - "name": "Input parameter", - "outputs": [], "position": { - "left": 676.3375507125828, - "top": 1426.4770174033545 + "left": 1214.1368049655293, + "top": 250.31238436598994 }, - "tool_id": null, - "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "a7391d09-c347-4520-91c2-8b07fd147efa", + "post_job_actions": { + "ChangeDatatypeActionoutput1": { + "action_arguments": { + "newtype": "fasta" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output1" + }, + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "tool_id": "CONVERTER_gz_to_uncompressed", + "tool_state": "{\"input1\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "81f21f4a-6c9c-4b8d-bb19-8a7343d77dc6", "when": null, "workflow_outputs": [] }, - "9": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 9, + "id": 15, "input_connections": { "input_param_type|input_param": { - "id": 8, - "output_name": "output" + "id": 13, + "output_name": "output_param_boolean" } }, "inputs": [], - "label": null, + "label": "No Gene track", "name": "Map parameter value", "outputs": [ { @@ -1451,8 +2452,8 @@ } ], "position": { - "left": 1443.6518169393487, - "top": 980.4294207784309 + "left": 1186.413509119842, + "top": 1363.2948622310325 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -1468,59 +2469,87 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": true, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": false, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "216d68c5-1d97-4dc5-961a-ea915c97a92d", + "uuid": "d8f71bf4-51a3-4af7-8cf2-fd16730469b4", "when": null, "workflow_outputs": [] }, - "10": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", "errors": null, - "id": 10, + "id": 16, "input_connections": { "assemblies_0|reference_genome|genome": { "id": 0, "output_name": "output" }, "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 2, - "output_name": "output" + "id": 12, + "output_name": "data_param" }, "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 3, + "id": 5, "output_name": "output" }, "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { - "id": 4, + "id": 6, "output_name": "output" }, "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 5, + "id": 7, "output_name": "output" }, "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 6, + "id": 8, "output_name": "output" }, "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 7, + "id": 9, "output_name": "output" }, "assemblies_1|reference_genome|genome": { + "id": 14, + "output_name": "output1" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 11, + "output_name": "data_param" + }, + "assemblies_2|reference_genome|genome": { "id": 1, "output_name": "output" }, - "when": { + "assemblies_2|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_2|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_2|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_2|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { "id": 8, "output_name": "output" + }, + "assemblies_2|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 9, + "output_name": "output" + }, + "when": { + "id": 13, + "output_name": "output_param_boolean" } }, "inputs": [], - "label": "JBrowse2 Hap1 and hap2 with 1st related species 2", + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", "name": "JBrowse2", "outputs": [ { @@ -1529,13 +2558,13 @@ } ], "position": { - "left": 2561.3898434899743, - "top": 900.6399388618673 + "left": 2604.560544371787, + "top": 306.40203071991476 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "JBrowse2 Single Haplotype with related species and Gene Tracks" + "newname": "JBrowse2 Hap1 and hap2 with related species and gene tracks" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -1548,56 +2577,80 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": []}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 2, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres Haplotype 2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "3.7.0+galaxy0", "type": "tool", - "uuid": "ffb776d2-dcb0-458c-9f2d-ffcd2de39ba2", + "uuid": "c4b25ca4-bdd4-4260-ac8b-80ae381da1ab", "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", "output_name": "output", - "uuid": "a71b266a-4d49-4dbd-b4d1-410849b941bb" + "uuid": "78b83679-2eea-4812-9936-54e27a2c404d" } ] }, - "11": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", "errors": null, - "id": 11, + "id": 17, "input_connections": { "assemblies_0|reference_genome|genome": { "id": 0, "output_name": "output" }, "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 2, - "output_name": "output" + "id": 12, + "output_name": "data_param" }, "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 3, + "id": 5, "output_name": "output" }, "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { - "id": 4, + "id": 6, "output_name": "output" }, "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 5, + "id": 7, "output_name": "output" }, "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 6, + "id": 8, "output_name": "output" }, "assemblies_1|reference_genome|genome": { + "id": 14, + "output_name": "output1" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 11, + "output_name": "data_param" + }, + "assemblies_2|reference_genome|genome": { "id": 1, "output_name": "output" }, + "assemblies_2|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_2|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_2|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 7, + "output_name": "output" + }, + "assemblies_2|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "output" + }, "when": { - "id": 9, + "id": 15, "output_name": "output_param_boolean" } }, @@ -1611,13 +2664,13 @@ } ], "position": { - "left": 1931.9531666252099, + "left": 1960.7191746063156, "top": 0 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "JBrowse2 Single Haplotype with related species" + "newname": "JBrowse2 Hap1 and hap2 with related species" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -1630,7 +2683,7 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": []}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 2, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres Haplotype 2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "3.7.0+galaxy0", "type": "tool", @@ -1638,160 +2691,730 @@ "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Single Haplotype with related species", + "label": "JBrowse2 Hap1 and hap2 with related species", "output_name": "output", - "uuid": "448fe2be-896a-49d7-b5c3-dfc4ceae0352" + "uuid": "ce6026de-ad8b-4dec-8926-fccc97f25df6" } ] } }, "tags": [], - "uuid": "236c7163-dde8-4597-a9b5-a7d55314997e" + "uuid": "e27defb2-86fb-4547-baf7-445ff2765428" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "e134915a-f5b7-4b32-a511-921e0b363bff", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 and hap2 with related species", + "output_name": "JBrowse2 Hap1 and hap2 with related species", + "uuid": "7562c81f-4b86-4932-8056-52f4dc17d2a9" + }, + { + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "uuid": "ca3249af-b46a-450d-8dbe-696490325d42" + } + ] + }, + "16": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "errors": null, + "id": 16, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 8, + "output_name": "mashout" + }, + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "assemblies_1|reference_genome|genome": { + "id": 0, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 3, + "output_name": "output" + }, + "assemblies_1|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "id": 4, + "output_name": "output" + }, + "assemblies_1|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 5, + "output_name": "output" + }, + "assemblies_1|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 6, + "output_name": "output" + }, + "when": { + "id": 13, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "JBrowse2 Hap1 vs Hap2", + "name": "JBrowse2", + "outputs": [ + { + "name": "output", + "type": "html" + } + ], + "position": { + "left": 2427.3955083914084, + "top": 105.84839360779135 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "JBrowse2 Hap1 vs Hap2" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_shed_repository": { + "changeset_revision": "bd903fbbc26e", + "name": "jbrowse2", + "owner": "fubar", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Alignments\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.7.0+galaxy0", + "type": "tool", + "uuid": "1838736c-68a4-41fd-b6c8-cd4de0aad595", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 vs Hap2", + "output_name": "output", + "uuid": "a3d1e37d-ea4d-44e6-ac96-c456fef1395f" + } + ] + } + }, + "tags": [], + "uuid": "db1e0e52-f223-4168-ae05-a4ba02ba34d1" + }, + "tool_id": null, + "type": "subworkflow", + "uuid": "c65e39fb-f036-47f7-9bd1-c63d161b736f", + "when": "$(inputs.when)", + "workflow_outputs": [ + { + "label": "JBrowse2 Hap1 vs Hap2", + "output_name": "JBrowse2 Hap1 vs Hap2", + "uuid": "a0cefb53-5c71-4e7a-8415-760c5f49d254" + }, + { + "label": "JBrowse2 Hap1 and hap2 with related species", + "output_name": "JBrowse2 Hap1 and hap2 with related species", + "uuid": "1d0f2614-f167-446d-b874-f2435995ca7a" + }, + { + "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "output_name": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "uuid": "42a88cd2-d2d5-4cfe-a00c-145d647cb12b" + }, + { + "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "uuid": "4a390dc0-8929-4bf5-aea4-2ca8352a8987" + } + ] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "Related Species": { + "id": 9, + "input_subworkflow_step_id": 0, + "output_name": "output" + }, + "when": { + "id": 13, + "output_name": "boolean_param" + } + }, + "inputs": [], + "label": null, + "name": "Validate No Duplicated names", + "outputs": [], + "position": { + "left": 2964.3431657962838, + "top": 245.025230274267 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6228-2785", + "name": "Patrik Smeds" + }, + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6421-3484", + "name": "Delphine Lariviere" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "Validate No Duplicated names", + "readme": "# JBrowse2 Precuration Tracks with Related Species Alignments\n\nThis workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species.\n\nThe workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser.\n\n## Inputs\n\n### Required Inputs\n\n1. **Species Name** [text] - Species identifier used in the assembly info report\n2. **Assembly Name** [text] - Assembly identifier (e.g., toLID)\n3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names)\n4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes)\n6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`).\n7. **Telomere P** [BED] - P-arm telomere coordinates\n8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty)\n9. **Gaps** [BED] - Assembly gap coordinates\n10. **Coverage** [BigWig] - PacBio HiFi read coverage track\n\n### Gene Annotation Options\n\n11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance\n12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled)\n\n## Outputs\n\n1. **Assembly Info** - Summary of species and assembly name\n2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used)\n3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included\n4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used)\n5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Additional outputs\n\nThese JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view.\n\n6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments\n7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included\n8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments\n9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Validation output\n\n10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas.\n\n## Usage Notes\n\n### Pairing with the Hi-C contact map workflow\n\nThis workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow:\n\n| Hi-C workflow output | Use here as input |\n|---|---|\n| `Decontaminated Hap1 with Suffix` | `Haplotype 1` |\n| `Decontaminated Hap2 with Suffix` | `Haplotype 2` |\n| `P telomeres bed` | `Telomere P` |\n| `Q telomeres Bed` | `Telomere Q` |\n| `Gaps Bed` | `Gaps` |\n| `BigWig Coverage` | `Coverage` |\n| `Compleasm Genes track` | `Genes` |\n\n### Related species selection\n\nChoose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection.\n\n**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example:\n\n```bash\nzcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz\n```\n\n### Scaffold name suffixes\n\nIf using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks.\n\n## Citation\n\nIf you use this workflow, please cite:\n- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z))\n- minimap2 (used for related-species alignment)\n- Other tools as listed in the workflow\n", + "report": { + "markdown": "# Precuration workflow on:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Info\")\n```\n\n## Duplication Stats\n\nSamtools markdup deduplication stats (if applicable)\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats\")\n```\n\n\n\nPairtools stats\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats: MultiQC\")\n```\n\n## Telomere report\n\n```galaxy\nhistory_dataset_embedded(output=\"Telomere Report\")\n```\n\n## Pretext Snapshots\n\nWith Multimapping\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks - Multimapping\")\n```\n\n\nWith MAPQ filtering\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks\")\n```\n\n\n" + }, + "steps": { + "0": { + "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 0.0, + "top": 587.3142014429646 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "b1d57707-483c-43cd-8256-0a2888af1246", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 1, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "data_param", + "type": "input" + } + ], + "position": { + "left": 453.18167963754297, + "top": 842.9610379933346 + }, + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_error\", \"__current_case__\": 2, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"RuntimeValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "c6317bbd-c7fd-424d-b2d5-5d9b0bae61df", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "CONVERTER_gz_to_uncompressed", + "errors": null, + "id": 2, + "input_connections": { + "input1": { + "id": 1, + "output_name": "data_param" + } + }, + "inputs": [], + "label": null, + "name": "Convert gz compressed file to uncompressed.", + "outputs": [ + { + "name": "output1", + "type": "auto" + } + ], + "position": { + "left": 832.2978216471757, + "top": 657.4627007832238 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput1": { + "action_arguments": { + "newtype": "fasta" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output1" + }, + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } }, - "tool_id": null, - "type": "subworkflow", - "uuid": "6ad9fa44-c0d3-49e8-af09-e1a93e66eb8a", + "tool_id": "CONVERTER_gz_to_uncompressed", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "6f868700-ff9c-4415-98d7-81befe9dde9e", "when": null, - "workflow_outputs": [ + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", + "errors": null, + "id": 3, + "input_connections": { + "infile": { + "id": 2, + "output_name": "output1" + } + }, + "inputs": [], + "label": null, + "name": "Search in textfiles", + "outputs": [ { - "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", - "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", - "uuid": "2dc05ed1-2c39-45a0-b07c-2ec4b8a6b0df" + "name": "output", + "type": "input" + } + ], + "position": { + "left": 1281.6271430795382, + "top": 516.9501479775356 + }, + "post_job_actions": { + "ChangeDatatypeActionoutput": { + "action_arguments": { + "newtype": "tabular" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output" }, - { - "label": "JBrowse2 Single Haplotype with related species", - "output_name": "JBrowse2 Single Haplotype with related species", - "uuid": "3c519fbb-453d-418c-8af3-e4532cf23c28" + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" } - ] + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \">\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "24671126-d835-4ecf-94c6-f22fa01d6abd", + "when": null, + "workflow_outputs": [] }, - "12": { + "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", "errors": null, - "id": 12, + "id": 4, "input_connections": { - "assemblies_0|reference_genome|genome": { - "id": 0, + "input_list": { + "id": 3, "output_name": "output" - }, - "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 2, + } + }, + "inputs": [], + "label": null, + "name": "Collapse Collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 1587.396456528243, + "top": 293.47025968475924 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "output" - }, - "assemblies_0|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { - "id": 3, + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", + "tool_shed_repository": { + "changeset_revision": "90981f86000f", + "name": "collapse_collections", + "owner": "nml", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "5.1.0", + "type": "tool", + "uuid": "6e2e1a5d-5849-4852-898d-6646c379ee0d", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy3", + "errors": null, + "id": 5, + "input_connections": { + "infile": { + "id": 4, "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Unique", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 1941.4028403619313, + "top": 0 + }, + "post_job_actions": { + "ChangeDatatypeActionoutfile": { + "action_arguments": { + "newtype": "tabular" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "outfile" }, - "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "4e7c4704-4734-49f8-b51e-53c500853bbc", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "wc_gnu", + "errors": null, + "id": 6, + "input_connections": { + "input1": { "id": 4, "output_name": "output" - }, - "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { + } + }, + "inputs": [], + "label": null, + "name": "Line/Word/Character count", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 1900.3906014415902, + "top": 510.6734558790175 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "wc_gnu", + "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "71d76ee3-7dac-450a-98e9-bb57111df8c5", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "wc_gnu", + "errors": null, + "id": 7, + "input_connections": { + "input1": { "id": 5, - "output_name": "output" + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Line/Word/Character count", + "outputs": [ + { + "name": "out_file1", + "type": "tabular" + } + ], + "position": { + "left": 2153.997360223585, + "top": 268.5825615907663 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "wc_gnu", + "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "2da84228-d818-493b-bafd-a95959ee2de3", + "when": null, + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 8, + "input_connections": { + "input1": { + "id": 6, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 2324.5531699243356, + "top": 502.9407403932288 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "c03bb38c-3383-4d3f-843f-9f74c70b1c47", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 9, + "input_connections": { + "input1": { + "id": 7, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 2437.4978065099026, + "top": 103.77316093552422 + }, + "post_job_actions": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + } + }, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "5ad8559e-e863-45e9-bae2-ede8be8314c7", + "when": null, + "workflow_outputs": [] + }, + "10": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", + "errors": null, + "id": 10, + "input_connections": { + "components_0|param_type|component_value": { + "id": 8, + "output_name": "integer_param" }, - "when": { + "components_1|param_type|component_value": { "id": 9, - "output_name": "output_param_boolean" + "output_name": "integer_param" } }, "inputs": [], - "label": "JBrowse2 Hap1", - "name": "JBrowse2", + "label": null, + "name": "Calculate numeric parameter value", "outputs": [ { - "name": "output", - "type": "html" + "name": "integer_param", + "type": "expression.json" } ], "position": { - "left": 1896.5312607039984, - "top": 0.0 + "left": 2820.8058443780224, + "top": 307.71874378596993 }, "post_job_actions": { - "RenameDatasetActionoutput": { + "HideDatasetActioninteger_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "integer_param" + }, + "RenameDatasetActioninteger_param": { "action_arguments": { - "newname": "JBrowse2 Single Haplotype" + "newname": "Number of Sequences with the same name" }, "action_type": "RenameDatasetAction", - "output_name": "output" + "output_name": "integer_param" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", "tool_shed_repository": { - "changeset_revision": "bd903fbbc26e", - "name": "jbrowse2", - "owner": "fubar", + "changeset_revision": "0e586762f97b", + "name": "calculate_numeric_param", + "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"-\"}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"\"}], \"output_type\": \"integer\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "3.7.0+galaxy0", + "tool_version": "0.1.0", "type": "tool", - "uuid": "bda6d01b-ed4d-44b5-9307-4113d25d704c", - "when": "$(inputs.when)", + "uuid": "bdc1a0bf-1614-47f8-90f8-89cc139edf9a", + "when": null, "workflow_outputs": [ { - "label": "JBrowse2 Single Haplotype", - "output_name": "output", - "uuid": "20eb67af-6a5e-44f1-a9eb-4cd7c7cf627a" + "label": "Number of Sequences with the same name", + "output_name": "integer_param", + "uuid": "7af4de2a-83be-44a2-a8de-b42d3501e405" } ] } }, "tags": [], - "uuid": "aa94bcea-e6b3-4677-9709-176f6f732c75" + "uuid": "02f7eddc-de0e-44ad-ade0-e505a0a98848" }, "tool_id": null, "type": "subworkflow", - "uuid": "b0c9d1b4-2cfe-46b6-8a59-e2bbf8418997", + "uuid": "171d269a-7197-40af-aa00-794b97d7e8c1", "when": "$(inputs.when)", - "workflow_outputs": [ - { - "label": "JBrowse2 Single Haplotype", - "output_name": "JBrowse2 Single Haplotype", - "uuid": "6a22e395-9c90-4c39-8649-a02200a5f9d3" - }, - { - "label": "JBrowse2 Single Haplotype with related species", - "output_name": "JBrowse2 Single Haplotype with related species", - "uuid": "0651be6a-3ad9-4302-a501-702a7d435ea4" - }, - { - "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", - "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", - "uuid": "010b5194-1e89-4f30-9b20-1e3d7eac7aeb" - }, - { - "label": "JBrowse2 Single Haplotype with Gene Track", - "output_name": "JBrowse2 Single Haplotype with Gene Track", - "uuid": "4eacbf80-e972-46c8-afe6-e90d72faa758" - } - ] + "workflow_outputs": [] }, - "19": { + "17": { "annotation": "", - "id": 19, + "id": 17, "input_connections": { "Coverage": { - "id": 10, - "input_subworkflow_step_id": 6, + "id": 8, + "input_subworkflow_step_id": 5, "output_name": "output" }, "Gaps": { - "id": 9, - "input_subworkflow_step_id": 5, + "id": 7, + "input_subworkflow_step_id": 4, "output_name": "output" }, "Genes": { - "id": 15, - "input_subworkflow_step_id": 8, - "output_name": "data_param" - }, - "Genes?": { - "id": 5, - "input_subworkflow_step_id": 7, + "id": 4, + "input_subworkflow_step_id": 6, "output_name": "output" }, "Hap1 fasta": { @@ -1799,45 +3422,40 @@ "input_subworkflow_step_id": 0, "output_name": "output" }, - "Hap2 fasta": { - "id": 14, - "input_subworkflow_step_id": 1, - "output_name": "data_param" - }, "Related Species": { - "id": 16, - "input_subworkflow_step_id": 2, - "output_name": "output1" + "id": 9, + "input_subworkflow_step_id": 1, + "output_name": "output" }, "Telomeres P": { - "id": 8, - "input_subworkflow_step_id": 4, + "id": 6, + "input_subworkflow_step_id": 3, "output_name": "output" }, "Telomeres Q": { - "id": 7, - "input_subworkflow_step_id": 3, + "id": 5, + "input_subworkflow_step_id": 2, "output_name": "output" }, "when": { - "id": 3, - "output_name": "output" + "id": 14, + "output_name": "output_param_boolean" } }, "inputs": [], "label": null, - "name": "Jbrowse for pre-curation", + "name": "Jbrowse for pre-curation single haplotype - 1 related Species ", "outputs": [], "position": { - "left": 3359.99060088773, - "top": 782.0624564807059 + "left": 2829.2929257523115, + "top": 965.6608835393258 }, "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", "comments": [], "format-version": "0.1", - "name": "Jbrowse for pre-curation", + "name": "Jbrowse for pre-curation single haplotype - 1 related Species ", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -1859,7 +3477,7 @@ "outputs": [], "position": { "left": 0, - "top": 85.5397415161874 + "top": 699.2443289019618 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -1878,21 +3496,21 @@ "inputs": [ { "description": "", - "name": "Hap2 fasta" + "name": "Related Species" } ], - "label": "Hap2 fasta", - "name": "Input dataset", + "label": "Related Species", + "name": "Input dataset collection", "outputs": [], "position": { - "left": 51.81545453466647, - "top": 205.03846714316876 + "left": 78.89568385575014, + "top": 794.3749846026999 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_state": "{\"optional\": true, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", "tool_version": null, - "type": "data_input", - "uuid": "177f6825-e58e-45e9-a3fc-8c7623187e02", + "type": "data_collection_input", + "uuid": "771229b7-cdcc-462a-a1e5-314204a3fca1", "when": null, "workflow_outputs": [] }, @@ -1905,21 +3523,21 @@ "inputs": [ { "description": "", - "name": "Related Species" + "name": "Telomeres Q" } ], - "label": "Related Species", - "name": "Input dataset collection", + "label": "Telomeres Q", + "name": "Input dataset", "outputs": [], "position": { - "left": 297.860981218189, - "top": 609.7270107228887 + "left": 162.91806250869854, + "top": 925.5453930768067 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", "tool_version": null, - "type": "data_collection_input", - "uuid": "20f7abfb-20b8-49bb-b522-cd911fd1ec4c", + "type": "data_input", + "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", "when": null, "workflow_outputs": [] }, @@ -1932,21 +3550,21 @@ "inputs": [ { "description": "", - "name": "Telomeres Q" + "name": "Telomeres P" } ], - "label": "Telomeres Q", + "label": "Telomeres P", "name": "Input dataset", "outputs": [], "position": { - "left": 347.4491076529599, - "top": 765.9971383218501 + "left": 235.76054218223504, + "top": 1049.1809061513864 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", "when": null, "workflow_outputs": [] }, @@ -1959,21 +3577,21 @@ "inputs": [ { "description": "", - "name": "Telomeres P" + "name": "Gaps" } ], - "label": "Telomeres P", + "label": "Gaps", "name": "Input dataset", "outputs": [], "position": { - "left": 455.5329585464028, - "top": 870.0948319299273 + "left": 325.8334374647798, + "top": 1143.422158149443 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", "when": null, "workflow_outputs": [] }, @@ -1986,21 +3604,21 @@ "inputs": [ { "description": "", - "name": "Gaps" + "name": "Coverage" } ], - "label": "Gaps", + "label": "Coverage", "name": "Input dataset", "outputs": [], "position": { - "left": 524.1536909971493, - "top": 963.4615908089734 + "left": 426.80614784345863, + "top": 1246.4956813108688 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "uuid": "738f43fc-5f88-4117-bcc3-4a9c1b01c0a1", "when": null, "workflow_outputs": [] }, @@ -2013,209 +3631,439 @@ "inputs": [ { "description": "", - "name": "Coverage" + "name": "Genes" } ], - "label": "Coverage", + "label": "Genes", "name": "Input dataset", "outputs": [], "position": { - "left": 581.1909253334677, - "top": 1050.5810577223672 + "left": 481.54024694955143, + "top": 1345.5356433169977 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", + "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "738f43fc-5f88-4117-bcc3-4a9c1b01c0a1", + "uuid": "3831fc6f-0526-46ab-869b-5a07c6cded67", "when": null, "workflow_outputs": [] }, "7": { "annotation": "", - "content_id": null, - "errors": null, "id": 7, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Genes?" + "input_connections": { + "Related Species": { + "id": 1, + "input_subworkflow_step_id": 0, + "output_name": "output" } - ], - "label": "Genes?", - "name": "Input parameter", + }, + "inputs": [], + "label": null, + "name": "Map Collection to boolean", "outputs": [], "position": { - "left": 632.8136499329014, - "top": 1153.233851898539 + "left": 1126.266841620324, + "top": 708.6678487625938 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6228-2785", + "name": "Patrik Smeds" + }, + { + "class": "Person", + "identifier": "https://orcid.org/0000-0001-6421-3484", + "name": "Delphine Lariviere" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "Map Collection to boolean", + "readme": "# JBrowse2 Precuration Tracks with Related Species Alignments\n\nThis workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species.\n\nThe workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser.\n\n## Inputs\n\n### Required Inputs\n\n1. **Species Name** [text] - Species identifier used in the assembly info report\n2. **Assembly Name** [text] - Assembly identifier (e.g., toLID)\n3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names)\n4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes)\n6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`).\n7. **Telomere P** [BED] - P-arm telomere coordinates\n8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty)\n9. **Gaps** [BED] - Assembly gap coordinates\n10. **Coverage** [BigWig] - PacBio HiFi read coverage track\n\n### Gene Annotation Options\n\n11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance\n12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled)\n\n## Outputs\n\n1. **Assembly Info** - Summary of species and assembly name\n2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used)\n3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included\n4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used)\n5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Additional outputs\n\nThese JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view.\n\n6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments\n7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included\n8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments\n9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Validation output\n\n10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas.\n\n## Usage Notes\n\n### Pairing with the Hi-C contact map workflow\n\nThis workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow:\n\n| Hi-C workflow output | Use here as input |\n|---|---|\n| `Decontaminated Hap1 with Suffix` | `Haplotype 1` |\n| `Decontaminated Hap2 with Suffix` | `Haplotype 2` |\n| `P telomeres bed` | `Telomere P` |\n| `Q telomeres Bed` | `Telomere Q` |\n| `Gaps Bed` | `Gaps` |\n| `BigWig Coverage` | `Coverage` |\n| `Compleasm Genes track` | `Genes` |\n\n### Related species selection\n\nChoose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection.\n\n**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example:\n\n```bash\nzcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz\n```\n\n### Scaffold name suffixes\n\nIf using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks.\n\n## Citation\n\nIf you use this workflow, please cite:\n- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z))\n- minimap2 (used for related-species alignment)\n- Other tools as listed in the workflow\n", + "report": { + "markdown": "# Precuration workflow on:\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Info\")\n```\n\n## Duplication Stats\n\nSamtools markdup deduplication stats (if applicable)\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats\")\n```\n\n\n\nPairtools stats\n```galaxy\nhistory_dataset_as_table(output=\"Hi-C duplication stats: MultiQC\")\n```\n\n## Telomere report\n\n```galaxy\nhistory_dataset_embedded(output=\"Telomere Report\")\n```\n\n## Pretext Snapshots\n\nWith Multimapping\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks - Multimapping\")\n```\n\n\nWith MAPQ filtering\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Snapshot With tracks\")\n```\n\n\n" + }, + "steps": { + "0": { + "annotation": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Note: Duplicated sequence names between the species in the collection will cause inaccurate alignment visualization in JBrowse2. ", + "name": "Related Species" + } + ], + "label": "Related Species", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 0, + "top": 0 + }, + "tool_id": null, + "tool_state": "{\"optional\": true, \"format\": [\"fasta.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "b1d57707-483c-43cd-8256-0a2888af1246", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 1, + "input_connections": { + "input_param_type|input_param": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": "Two Haplotypes 2", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_boolean", + "type": "expression.json" + } + ], + "position": { + "left": 507.52614703835707, + "top": 68.65082494054082 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "30ef2c07-c458-4a90-94b7-5e5ae4885844", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "errors": null, + "id": 2, + "input_connections": { + "input_param_type|input_param": { + "id": 1, + "output_name": "output_param_boolean" + } + }, + "inputs": [], + "label": "Two Haplotypes 3", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_text", + "type": "expression.json" + } + ], + "position": { + "left": 801.9711946226973, + "top": 268.066568476228 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + }, + "HideDatasetActionoutput_param_text": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_text" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "5be371df-1c67-42ae-a535-da4ca4bf1e51", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3", + "errors": null, + "id": 3, + "input_connections": { + "token_set_0|line": { + "id": 2, + "output_name": "output_param_text" + } + }, + "inputs": [], + "label": null, + "name": "Create text file", + "outputs": [ + { + "name": "outfile", + "type": "txt" + } + ], + "position": { + "left": 1031.2529071684971, + "top": 141.25993418553026 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": {\"__class__\": \"ConnectedValue\"}, \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "f2c6b8fd-f348-494d-867e-28d82492a589", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3", + "errors": null, + "id": 4, + "input_connections": { + "inputs": { + "id": 3, + "output_name": "outfile" + } + }, + "inputs": [], + "label": null, + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1404.1850282401706, + "top": 159.59233303291586 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3", + "tool_shed_repository": { + "changeset_revision": "ab83aa685821", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", + "type": "tool", + "uuid": "951df8ae-cb04-448c-9b26-1b1c72e52354", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "Show beginning1", + "errors": null, + "id": 5, + "input_connections": { + "input": { + "id": 4, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Select first", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 1591.5813587970113, + "top": 415.32944461901855 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "Show beginning1", + "tool_state": "{\"header\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineNum\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.2", + "type": "tool", + "uuid": "6777b035-d40f-471e-b677-c886520c5f08", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "param_value_from_file", + "errors": null, + "id": 6, + "input_connections": { + "input1": { + "id": 5, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Parse parameter value", + "outputs": [ + { + "name": "boolean_param", + "type": "expression.json" + } + ], + "position": { + "left": 1900.9513665053723, + "top": 426.5056982072265 + }, + "post_job_actions": {}, + "tool_id": "param_value_from_file", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"boolean\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.1.0", + "type": "tool", + "uuid": "39916b95-3287-497f-83ea-822bb970a388", + "when": null, + "workflow_outputs": [ + { + "label": "boolean_param", + "output_name": "boolean_param", + "uuid": "651aac03-f463-4bb0-bae9-c1e6d0d808d8" + } + ] + } + }, + "tags": [], + "uuid": "877369eb-5f6e-4a0f-9519-c6f3bb328653" }, "tool_id": null, - "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "7c8dc365-9ea0-4f5a-af57-0983008b7ade", + "type": "subworkflow", + "uuid": "e94777b6-3b4b-495c-8225-154261540382", "when": null, "workflow_outputs": [] }, "8": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, "id": 8, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Genes" - } - ], - "label": "Genes", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 683.9939626471161, - "top": 1243.3922887919446 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "dabdef6f-cb85-410c-a5ef-229d9ae21a3b", - "when": null, - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", - "errors": null, - "id": 9, "input_connections": { - "query": { - "id": 0, - "output_name": "output" - }, - "reflist": { - "id": 1, + "input_param_type|input_param": { + "id": 6, "output_name": "output" } }, "inputs": [], - "label": "Align Haplotypes Hap1 is query", - "name": "mashmap", + "label": null, + "name": "Map parameter value", "outputs": [ { - "name": "mashout", - "type": "paf" + "name": "output_param_boolean", + "type": "expression.json" } ], "position": { - "left": 1507.3273804321968, - "top": 793.8614046625582 + "left": 859.5308837376912, + "top": 354.3262966418495 }, "post_job_actions": { - "HideDatasetActionmashout": { + "HideDatasetActionoutput_param_boolean": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "mashout" - }, - "RenameDatasetActionmashout": { - "action_arguments": { - "newname": "Alignment Hap1 vs Hap2" - }, - "action_type": "RenameDatasetAction", - "output_name": "mashout" + "output_name": "output_param_boolean" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "tool_shed_repository": { - "changeset_revision": "a3a6b0b31f2d", - "name": "mashmap", + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"dense\": false, \"filter_mode\": \"map\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"90.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "3.1.3+galaxy0", + "tool_version": "0.2.0", "type": "tool", - "uuid": "c7740c1c-5674-43d4-aa00-aeca2dcc7fa6", + "uuid": "881a5654-873e-43f9-8731-3023ec1bea9b", "when": null, "workflow_outputs": [] }, - "10": { + "9": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", "errors": null, - "id": 10, + "id": 9, "input_connections": { "query": { "id": 0, "output_name": "output" }, - "reflist": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "label": "Hap1 vs Species", - "name": "mashmap", - "outputs": [ - { - "name": "mashout", - "type": "paf" - } - ], - "position": { - "left": 1211.2240968936799, - "top": 0 - }, - "post_job_actions": { - "HideDatasetActionmashout": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "mashout" - }, - "RenameDatasetActionmashout": { - "action_arguments": { - "newname": "Species to Hap2" - }, - "action_type": "RenameDatasetAction", - "output_name": "mashout" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", - "tool_shed_repository": { - "changeset_revision": "a3a6b0b31f2d", - "name": "mashmap", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"dense\": false, \"filter_mode\": \"one-to-one\", \"kmerComplexity\": null, \"kmerThreshold\": null, \"noHgFilter\": false, \"noMerge\": false, \"perc_identity\": \"85.0\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reflist\": {\"__class__\": \"ConnectedValue\"}, \"reportPercentage\": false, \"seqLength\": \"5000\", \"sketchSize\": \"0\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "3.1.3+galaxy0", - "type": "tool", - "uuid": "ba8fe065-a989-4cff-bcda-2e6883b1f6cd", - "when": null, - "workflow_outputs": [] - }, - "11": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0", - "errors": null, - "id": 11, - "input_connections": { - "query": { - "id": 2, - "output_name": "output" - }, "reflist": { "id": 1, "output_name": "output" + }, + "when": { + "id": 7, + "output_name": "boolean_param" } }, "inputs": [], - "label": "Species vs Hap2", + "label": "hap1 vs species", "name": "mashmap", "outputs": [ { @@ -2224,8 +4072,8 @@ } ], "position": { - "left": 1225.3530086334274, - "top": 365.8375864791642 + "left": 1748.7451070250318, + "top": 1065.6902746606195 }, "post_job_actions": { "HideDatasetActionmashout": { @@ -2235,7 +4083,7 @@ }, "RenameDatasetActionmashout": { "action_arguments": { - "newname": "Species to Hap2" + "newname": "hap1 vs species" }, "action_type": "RenameDatasetAction", "output_name": "mashout" @@ -2252,19 +4100,19 @@ "tool_uuid": null, "tool_version": "3.1.3+galaxy0", "type": "tool", - "uuid": "cf1e95b5-3bd6-41c1-a2d4-93ac6c1b1b1a", - "when": null, + "uuid": "b1a857dd-1140-4641-943b-cb141b6a6f81", + "when": "$(inputs.when)", "workflow_outputs": [] }, - "12": { + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 12, + "id": 10, "input_connections": { "input_param_type|input_param": { - "id": 7, - "output_name": "output" + "id": 8, + "output_name": "output_param_boolean" } }, "inputs": [], @@ -2277,8 +4125,8 @@ } ], "position": { - "left": 1107.9772160860653, - "top": 1163.288147730554 + "left": 1152.7909069113884, + "top": 306.13159851542645 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -2294,33 +4142,33 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": true, \"to\": \"False\"}, {\"__index__\": 1, \"from\": false, \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": true, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "03bd04b4-815e-471e-8bf2-b51054b8390e", + "uuid": "a8eddf6e-6019-46b9-bda4-3cae4f66baf1", "when": null, "workflow_outputs": [] }, - "13": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", "errors": null, - "id": 13, + "id": 11, "input_connections": { "assemblies_0|reference_genome|genome": { "id": 0, "output_name": "output" }, "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 9, - "output_name": "mashout" + "id": 2, + "output_name": "output" }, - "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { "id": 3, "output_name": "output" }, - "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { "id": 4, "output_name": "output" }, @@ -2332,41 +4180,13 @@ "id": 6, "output_name": "output" }, - "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 8, - "output_name": "output" - }, - "assemblies_1|reference_genome|genome": { - "id": 0, - "output_name": "output" - }, - "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 3, - "output_name": "output" - }, - "assemblies_1|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { - "id": 4, - "output_name": "output" - }, - "assemblies_1|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 5, - "output_name": "output" - }, - "assemblies_1|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 6, - "output_name": "output" - }, - "assemblies_1|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 8, - "output_name": "output" - }, "when": { - "id": 7, - "output_name": "output" + "id": 8, + "output_name": "output_param_boolean" } }, "inputs": [], - "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "label": "JBrowse2 Hap1 with gene track", "name": "JBrowse2", "outputs": [ { @@ -2375,13 +4195,13 @@ } ], "position": { - "left": 2146.8088643141236, - "top": 602.2449366027035 + "left": 2283.70977067512, + "top": 41.012471287696755 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "JBrowse2 Hap1 vs Hap2 with gene tracks" + "newname": "JBrowse2 Single Haplotype with Gene Track" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -2394,42 +4214,37 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Alignments\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "3.7.0+galaxy0", "type": "tool", - "uuid": "8579f589-f836-4f8e-ad72-aa14a8b6c450", + "uuid": "8244bcfd-113f-4a5f-8b7a-4ebf39a2fd0d", "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", + "label": "JBrowse2 Single Haplotype with Gene Track", "output_name": "output", - "uuid": "4db7f57b-58ba-4932-9d15-8a0e3cde1f9b" + "uuid": "b4b0f191-314c-4519-8ea9-6885a3c3a1e5" } ] }, - "14": { + "12": { "annotation": "", - "id": 14, + "id": 12, "input_connections": { "Coverage": { - "id": 6, - "input_subworkflow_step_id": 8, - "output_name": "output" - }, - "Gaps": { "id": 5, - "input_subworkflow_step_id": 7, + "input_subworkflow_step_id": 6, "output_name": "output" }, - "Genes": { - "id": 8, - "input_subworkflow_step_id": 10, + "Gaps": { + "id": 4, + "input_subworkflow_step_id": 5, "output_name": "output" }, - "Genes?": { - "id": 7, - "input_subworkflow_step_id": 9, + "Gene Tracks": { + "id": 6, + "input_subworkflow_step_id": 7, "output_name": "output" }, "Hap1 fasta": { @@ -2438,50 +4253,44 @@ "output_name": "output" }, "Hap1 vs Species": { - "id": 10, - "input_subworkflow_step_id": 4, + "id": 9, + "input_subworkflow_step_id": 2, "output_name": "mashout" }, - "Hap2 fasta": { + "Related Fasta": { "id": 1, "input_subworkflow_step_id": 1, "output_name": "output" }, - "Related Species": { - "id": 2, - "input_subworkflow_step_id": 2, - "output_name": "output" - }, - "Species vs Hap2": { - "id": 11, - "input_subworkflow_step_id": 3, - "output_name": "mashout" - }, "Telomeres P": { - "id": 4, - "input_subworkflow_step_id": 6, + "id": 3, + "input_subworkflow_step_id": 4, "output_name": "output" }, "Telomeres Q": { - "id": 3, - "input_subworkflow_step_id": 5, + "id": 2, + "input_subworkflow_step_id": 3, "output_name": "output" + }, + "when": { + "id": 7, + "output_name": "boolean_param" } }, "inputs": [], "label": null, - "name": "Jbrowse2 for 1 related species", + "name": "Jbrowse2 for 1 related species - single haplotype", "outputs": [], "position": { - "left": 1887.4863910257557, - "top": 102.53355703483975 + "left": 2229.6998454459986, + "top": 1230.1735808481742 }, "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", "comments": [], "format-version": "0.1", - "name": "Jbrowse2 for 1 related species", + "name": "Jbrowse2 for 1 related species - single haplotype", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -2503,7 +4312,7 @@ "outputs": [], "position": { "left": 0, - "top": 271.13908772215916 + "top": 209.22223652047438 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -2522,21 +4331,21 @@ "inputs": [ { "description": "", - "name": "Hap2 fasta" + "name": "Related Fasta" } ], - "label": "Hap2 fasta", + "label": "Related Fasta", "name": "Input dataset", "outputs": [], "position": { - "left": 53.14881800970572, - "top": 420.7641795440555 + "left": 64.19044612855507, + "top": 339.63559170456904 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_state": "{\"optional\": true, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "177f6825-e58e-45e9-a3fc-8c7623187e02", + "uuid": "385825a9-198e-425f-9fb3-55af892d20dc", "when": null, "workflow_outputs": [] }, @@ -2549,21 +4358,21 @@ "inputs": [ { "description": "", - "name": "Related Species" + "name": "Hap1 vs Species" } ], - "label": "Related Species", + "label": "Hap1 vs Species", "name": "Input dataset", "outputs": [], "position": { - "left": 98.91709918730632, - "top": 553.1054764799819 + "left": 113.31939864522589, + "top": 479.1639618101156 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", + "tool_state": "{\"optional\": true, \"format\": [\"paf\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "604a6bec-8c1f-47e3-8884-c32f63246589", + "uuid": "c18b3a25-89e8-4853-81fe-affb519a9ae0", "when": null, "workflow_outputs": [] }, @@ -2576,21 +4385,21 @@ "inputs": [ { "description": "", - "name": "Species vs Hap2" + "name": "Telomeres Q" } ], - "label": "Species vs Hap2", + "label": "Telomeres Q", "name": "Input dataset", "outputs": [], "position": { - "left": 147.9198303415696, - "top": 670.2931389328182 + "left": 173.91872965677103, + "top": 640.6573469993632 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"paf\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "ebdc47b3-16f5-48e9-a101-c82b2370181a", + "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", "when": null, "workflow_outputs": [] }, @@ -2603,21 +4412,21 @@ "inputs": [ { "description": "", - "name": "Hap1 vs Species" + "name": "Telomeres P" } ], - "label": "Hap1 vs Species", + "label": "Telomeres P", "name": "Input dataset", "outputs": [], "position": { - "left": 175.64670268098203, - "top": 777.2105888619357 + "left": 262.08020244071406, + "top": 799.4536221643712 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"paf\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "385825a9-198e-425f-9fb3-55af892d20dc", + "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", "when": null, "workflow_outputs": [] }, @@ -2630,21 +4439,21 @@ "inputs": [ { "description": "", - "name": "Telomeres Q" + "name": "Gaps" } ], - "label": "Telomeres Q", + "label": "Gaps", "name": "Input dataset", "outputs": [], "position": { - "left": 206.21568172170709, - "top": 895.0983900914266 + "left": 334.3294215467986, + "top": 926.268574398666 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "ce01ac46-a3c2-4013-ba5b-ea8a0e46be64", + "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", "when": null, "workflow_outputs": [] }, @@ -2657,21 +4466,21 @@ "inputs": [ { "description": "", - "name": "Telomeres P" + "name": "Coverage" } ], - "label": "Telomeres P", + "label": "Coverage", "name": "Input dataset", "outputs": [], "position": { - "left": 274.77222990165984, - "top": 1069.4502766623036 + "left": 431.83941564925703, + "top": 1078.7178133506623 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "8044ff06-8a3b-4ac1-b6ee-521cc28e585d", + "uuid": "2131fd1e-4f34-4662-be5c-382101fcbc76", "when": null, "workflow_outputs": [] }, @@ -2684,118 +4493,222 @@ "inputs": [ { "description": "", - "name": "Gaps" + "name": "Gene Tracks" } ], - "label": "Gaps", + "label": "Gene Tracks", "name": "Input dataset", "outputs": [], "position": { - "left": 353.8919295731858, - "top": 1244.9653893778952 + "left": 541.5464695972953, + "top": 1218.2490175701384 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\"}", + "tool_state": "{\"optional\": true, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "37e56713-8aa6-474e-9a87-6c702d7d6b49", + "uuid": "f6db855c-e1de-49f7-836c-87a510e955aa", "when": null, "workflow_outputs": [] }, "8": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, "id": 8, - "input_connections": {}, - "inputs": [ + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ { - "description": "", - "name": "Coverage" + "name": "data_param", + "type": "input" } ], - "label": "Coverage", - "name": "Input dataset", - "outputs": [], "position": { - "left": 391.49614814580605, - "top": 1410.3962329181184 + "left": 514.7385434096283, + "top": 319.35295187850693 + }, + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_error\", \"__current_case__\": 2, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "30d3a9e5-b5b0-4e04-8950-74c3c0c6f772", + "when": null, + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "errors": null, + "id": 9, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "data_param", + "type": "input" + } + ], + "position": { + "left": 791.7095008745389, + "top": 702.9542201693089 + }, + "post_job_actions": { + "HideDatasetActiondata_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "data_param" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"bigwig\"], \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "2131fd1e-4f34-4662-be5c-382101fcbc76", + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_error\", \"__current_case__\": 2, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "e8b2b609-6fb6-4708-806f-9bc519806d6f", "when": null, "workflow_outputs": [] }, - "9": { + "10": { "annotation": "", - "content_id": null, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 9, - "input_connections": {}, - "inputs": [ + "id": 10, + "input_connections": { + "input_param_type|input_param": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Map parameter value", + "outputs": [ { - "description": "", - "name": "Genes?" + "name": "output_param_boolean", + "type": "expression.json" } ], - "label": "Genes?", - "name": "Input parameter", - "outputs": [], "position": { - "left": 419.6781495431659, - "top": 1559.6965461441787 + "left": 1047.1756169820526, + "top": 1156.3320897874444 }, - "tool_id": null, - "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "ccb4de54-c370-4f56-a5d4-42708ee6c835", + "post_job_actions": { + "HideDatasetActionoutput_param_boolean": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_boolean" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"data\", \"__current_case__\": 4, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": []}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "0.2.0", + "type": "tool", + "uuid": "480c228f-4d21-48c2-8786-920c43590c72", "when": null, "workflow_outputs": [] }, - "10": { + "11": { "annotation": "", - "content_id": null, + "content_id": "CONVERTER_gz_to_uncompressed", "errors": null, - "id": 10, - "input_connections": {}, - "inputs": [ + "id": 11, + "input_connections": { + "input1": { + "id": 8, + "output_name": "data_param" + } + }, + "inputs": [], + "label": null, + "name": "Convert gz compressed file to uncompressed.", + "outputs": [ { - "description": "", - "name": "Genes" + "name": "output1", + "type": "auto" } ], - "label": "Genes", - "name": "Input dataset", - "outputs": [], "position": { - "left": 450.73254127706855, - "top": 1696.059196784704 + "left": 907.1606030128123, + "top": 121.02662028802301 }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "496c7358-def1-4256-b4e8-6698cac34f97", + "post_job_actions": { + "ChangeDatatypeActionoutput1": { + "action_arguments": { + "newtype": "fasta" + }, + "action_type": "ChangeDatatypeAction", + "output_name": "output1" + }, + "HideDatasetActionoutput1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "tool_id": "CONVERTER_gz_to_uncompressed", + "tool_state": "{\"input1\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.0.0", + "type": "tool", + "uuid": "17100313-6cd1-4992-89f6-d2136fbd2cc9", "when": null, "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 11, + "id": 12, "input_connections": { "input_param_type|input_param": { - "id": 9, - "output_name": "output" + "id": 10, + "output_name": "output_param_boolean" } }, "inputs": [], - "label": "No Gene track", + "label": null, "name": "Map parameter value", "outputs": [ { @@ -2804,8 +4717,8 @@ } ], "position": { - "left": 1030.3127513910322, - "top": 1346.1174612746302 + "left": 1443.640629349266, + "top": 980.955490296477 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -2821,87 +4734,59 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": false, \"to\": \"True\"}, {\"__index__\": 1, \"from\": false, \"to\": \"False\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"boolean\", \"__current_case__\": 3, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": true, \"to\": \"False\"}, {\"__index__\": 1, \"from\": false, \"to\": \"True\"}]}, \"output_param_type\": \"boolean\", \"unmapped\": {\"on_unmapped\": \"input\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "0.2.0", "type": "tool", - "uuid": "d8f71bf4-51a3-4af7-8cf2-fd16730469b4", + "uuid": "216d68c5-1d97-4dc5-961a-ea915c97a92d", "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", "errors": null, - "id": 12, + "id": 13, "input_connections": { "assemblies_0|reference_genome|genome": { "id": 0, "output_name": "output" }, "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 4, - "output_name": "output" + "id": 9, + "output_name": "data_param" }, "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 5, + "id": 3, "output_name": "output" }, "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { - "id": 6, + "id": 4, "output_name": "output" }, "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 7, - "output_name": "output" - }, - "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 8, - "output_name": "output" - }, - "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 10, - "output_name": "output" - }, - "assemblies_1|reference_genome|genome": { - "id": 2, - "output_name": "output" - }, - "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 3, - "output_name": "output" - }, - "assemblies_2|reference_genome|genome": { - "id": 1, - "output_name": "output" - }, - "assemblies_2|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { "id": 5, "output_name": "output" }, - "assemblies_2|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { "id": 6, "output_name": "output" }, - "assemblies_2|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_4|data_tracks_0|data_format|annotation_cond|annotation": { "id": 7, "output_name": "output" }, - "assemblies_2|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 8, - "output_name": "output" - }, - "assemblies_2|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 10, - "output_name": "output" + "assemblies_1|reference_genome|genome": { + "id": 11, + "output_name": "output1" }, "when": { - "id": 9, - "output_name": "output" + "id": 10, + "output_name": "output_param_boolean" } }, "inputs": [], - "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "label": "JBrowse2 Hap1 and hap2 with 1st related species 2", "name": "JBrowse2", "outputs": [ { @@ -2910,13 +4795,13 @@ } ], "position": { - "left": 2604.560544371787, - "top": 306.40203071991476 + "left": 2561.3748868997627, + "top": 901.9506006750755 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "JBrowse2 Hap1 and hap2 with related species and gene tracks" + "newname": "JBrowse2 Single Haplotype with related species and Gene Tracks" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -2929,80 +4814,56 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 2, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres Haplotype 2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"Annotations\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"RuntimeValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 4, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": []}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "3.7.0+galaxy0", "type": "tool", - "uuid": "c4b25ca4-bdd4-4260-ac8b-80ae381da1ab", + "uuid": "ffb776d2-dcb0-458c-9f2d-ffcd2de39ba2", "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", + "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", "output_name": "output", - "uuid": "78b83679-2eea-4812-9936-54e27a2c404d" + "uuid": "a71b266a-4d49-4dbd-b4d1-410849b941bb" } ] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", "errors": null, - "id": 13, + "id": 14, "input_connections": { "assemblies_0|reference_genome|genome": { "id": 0, "output_name": "output" }, "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 4, - "output_name": "output" + "id": 9, + "output_name": "data_param" }, "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 5, + "id": 3, "output_name": "output" }, "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { - "id": 6, + "id": 4, "output_name": "output" }, "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 7, - "output_name": "output" - }, - "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 8, - "output_name": "output" - }, - "assemblies_1|reference_genome|genome": { - "id": 2, - "output_name": "output" - }, - "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 3, - "output_name": "output" - }, - "assemblies_2|reference_genome|genome": { - "id": 1, - "output_name": "output" - }, - "assemblies_2|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { "id": 5, "output_name": "output" }, - "assemblies_2|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { "id": 6, "output_name": "output" }, - "assemblies_2|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 7, - "output_name": "output" - }, - "assemblies_2|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 8, - "output_name": "output" + "assemblies_1|reference_genome|genome": { + "id": 11, + "output_name": "output1" }, "when": { - "id": 11, + "id": 12, "output_name": "output_param_boolean" } }, @@ -3016,13 +4877,13 @@ } ], "position": { - "left": 1960.7191746063156, + "left": 1931.9531666252099, "top": 0 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "JBrowse2 Hap1 and hap2 with related species" + "newname": "JBrowse2 Single Haplotype with related species" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -3035,7 +4896,7 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 2, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres Haplotype 2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Synteny Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": []}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "3.7.0+galaxy0", "type": "tool", @@ -3043,90 +4904,66 @@ "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Hap1 and hap2 with related species", + "label": "JBrowse2 Single Haplotype with related species", "output_name": "output", - "uuid": "ce6026de-ad8b-4dec-8926-fccc97f25df6" + "uuid": "448fe2be-896a-49d7-b5c3-dfc4ceae0352" } ] } }, "tags": [], - "uuid": "fb028d13-e1d0-4d81-b413-b2c662d5213a" + "uuid": "3f60b623-c574-44bf-a302-0d6f0dca499f" }, "tool_id": null, "type": "subworkflow", - "uuid": "e134915a-f5b7-4b32-a511-921e0b363bff", - "when": null, + "uuid": "6ad9fa44-c0d3-49e8-af09-e1a93e66eb8a", + "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "uuid": "ca3249af-b46a-450d-8dbe-696490325d42" + "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "uuid": "2dc05ed1-2c39-45a0-b07c-2ec4b8a6b0df" }, { - "label": "JBrowse2 Hap1 and hap2 with related species", - "output_name": "JBrowse2 Hap1 and hap2 with related species", - "uuid": "7562c81f-4b86-4932-8056-52f4dc17d2a9" + "label": "JBrowse2 Single Haplotype with related species", + "output_name": "JBrowse2 Single Haplotype with related species", + "uuid": "3c519fbb-453d-418c-8af3-e4532cf23c28" } ] }, - "15": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", - "errors": null, - "id": 15, - "input_connections": { - "assemblies_0|reference_genome|genome": { - "id": 0, - "output_name": "output" - }, - "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 9, - "output_name": "mashout" - }, - "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 3, - "output_name": "output" - }, - "assemblies_0|track_groups_1|data_tracks_1|data_format|annotation_cond|annotation": { - "id": 4, - "output_name": "output" - }, - "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 5, - "output_name": "output" - }, - "assemblies_0|track_groups_3|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 6, + "errors": null, + "id": 13, + "input_connections": { + "assemblies_0|reference_genome|genome": { + "id": 0, "output_name": "output" }, - "assemblies_1|reference_genome|genome": { - "id": 0, + "assemblies_0|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "id": 2, "output_name": "output" }, - "assemblies_1|track_groups_0|data_tracks_0|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { "id": 3, "output_name": "output" }, - "assemblies_1|track_groups_0|data_tracks_1|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { "id": 4, "output_name": "output" }, - "assemblies_1|track_groups_1|data_tracks_0|data_format|annotation_cond|annotation": { + "assemblies_0|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { "id": 5, "output_name": "output" }, - "assemblies_1|track_groups_2|data_tracks_0|data_format|annotation_cond|annotation": { - "id": 6, - "output_name": "output" - }, "when": { - "id": 12, + "id": 10, "output_name": "output_param_boolean" } }, "inputs": [], - "label": "JBrowse2 Hap1 vs Hap2", + "label": "JBrowse2 Hap1", "name": "JBrowse2", "outputs": [ { @@ -3135,13 +4972,13 @@ } ], "position": { - "left": 2427.3955083914084, - "top": 101.59146846369417 + "left": 1896.5312607039984, + "top": 0 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "JBrowse2 Hap1 vs Hap2" + "newname": "JBrowse2 Single Haplotype" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -3154,369 +4991,64 @@ "owner": "fubar", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Alignments\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"synteny\", \"__current_case__\": 7, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearSyntenyDisplay\", \"__current_case__\": 1}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Telomeres Hap1\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 3, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}, {\"__index__\": 1, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"assemblies\": [{\"__index__\": 0, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"defaultLocation\": \"\", \"ref_name_aliases\": {\"__class__\": \"RuntimeValue\"}, \"cytobands\": {\"__class__\": \"RuntimeValue\"}, \"track_groups\": [{\"__index__\": 0, \"category\": \"Telomeres\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Gaps\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 0, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"index\": false, \"jbstyle\": {\"track_style\": {\"display\": \"LinearBasicDisplay\", \"__current_case__\": 0, \"display_mode\": \"normal\", \"show_labels\": true, \"labels_name\": \"jexl:get(feature,'name') || get(feature,'id')\", \"show_descriptions\": true, \"descriptions_name\": \"jexl:get(feature,'note') || get(feature,'description')\", \"max_height\": \"600\"}}, \"formatdetails\": {\"formatdetails_feature\": null, \"formatdetails_subfeature\": null, \"formatdetails_depth\": \"1\"}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}, {\"__index__\": 2, \"category\": \"HiFi Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 3, \"annotation_cond\": {\"annotation_source\": \"history\", \"__current_case__\": 0, \"annotation\": {\"__class__\": \"ConnectedValue\"}}, \"jbstyle\": {\"track_style\": {\"display\": \"LinearWiggleDisplay\", \"__current_case__\": 0, \"wig_renderer\": \"xyplot\"}}, \"metadata\": {\"galaxy_metadata\": true, \"metadata_bonus\": {\"__class__\": \"RuntimeValue\"}}, \"track_visibility\": \"default_on\"}}]}]}], \"jbgen\": {\"enableAnalytics\": false, \"primary_color\": \"#0d233f\", \"secondary_color\": \"#721e63\", \"tertiary_color\": \"#135560\", \"quaternary_color\": \"#ffb11d\", \"font_size\": \"10\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, "tool_version": "3.7.0+galaxy0", "type": "tool", - "uuid": "1838736c-68a4-41fd-b6c8-cd4de0aad595", + "uuid": "bda6d01b-ed4d-44b5-9307-4113d25d704c", "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Hap1 vs Hap2", + "label": "JBrowse2 Single Haplotype", "output_name": "output", - "uuid": "a3d1e37d-ea4d-44e6-ac96-c456fef1395f" + "uuid": "20eb67af-6a5e-44f1-a9eb-4cd7c7cf627a" } ] } }, "tags": [], - "uuid": "feda97a2-4c3f-4211-80f4-3c4cd83555a0" + "uuid": "86fc2aa8-bf64-4e3f-a515-b2bcd0166c65" }, "tool_id": null, "type": "subworkflow", - "uuid": "c65e39fb-f036-47f7-9bd1-c63d161b736f", + "uuid": "b0c9d1b4-2cfe-46b6-8a59-e2bbf8418997", "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "output_name": "JBrowse2 Hap1 and hap2 with related species and gene tracks", - "uuid": "4a390dc0-8929-4bf5-aea4-2ca8352a8987" + "label": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "output_name": "JBrowse2 Single Haplotype with related species and Gene Tracks", + "uuid": "010b5194-1e89-4f30-9b20-1e3d7eac7aeb" }, { - "label": "JBrowse2 Hap1 and hap2 with related species", - "output_name": "JBrowse2 Hap1 and hap2 with related species", - "uuid": "1d0f2614-f167-446d-b874-f2435995ca7a" + "label": "JBrowse2 Single Haplotype with related species", + "output_name": "JBrowse2 Single Haplotype with related species", + "uuid": "0651be6a-3ad9-4302-a501-702a7d435ea4" }, { - "label": "JBrowse2 Hap1 vs Hap2", - "output_name": "JBrowse2 Hap1 vs Hap2", - "uuid": "a0cefb53-5c71-4e7a-8415-760c5f49d254" + "label": "JBrowse2 Single Haplotype", + "output_name": "JBrowse2 Single Haplotype", + "uuid": "6a22e395-9c90-4c39-8649-a02200a5f9d3" }, { - "label": "JBrowse2 Hap1 vs Hap2 with gene tracks", - "output_name": "JBrowse2 Hap1 vs Hap2 with gene tracks", - "uuid": "42a88cd2-d2d5-4cfe-a00c-145d647cb12b" + "label": "JBrowse2 Single Haplotype with Gene Track", + "output_name": "JBrowse2 Single Haplotype with Gene Track", + "uuid": "4eacbf80-e972-46c8-afe6-e90d72faa758" } ] }, - "20": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", - "errors": null, - "id": 20, - "input_connections": { - "input_list": { - "id": 17, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Collapse Collection", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 2499.556473225303, - "top": 293.47025968475924 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", - "tool_shed_repository": { - "changeset_revision": "90981f86000f", - "name": "collapse_collections", - "owner": "nml", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "5.1.0", - "type": "tool", - "uuid": "6e2e1a5d-5849-4852-898d-6646c379ee0d", - "when": null, - "workflow_outputs": [] - }, - "21": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy3", - "errors": null, - "id": 21, - "input_connections": { - "infile": { - "id": 20, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Unique", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 2853.562857058991, - "top": 0 - }, - "post_job_actions": { - "ChangeDatatypeActionoutfile": { - "action_arguments": { - "newtype": "tabular" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "outfile" - }, - "HideDatasetActionoutfile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy3", - "tool_shed_repository": { - "changeset_revision": "ab83aa685821", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "9.5+galaxy3", - "type": "tool", - "uuid": "4e7c4704-4734-49f8-b51e-53c500853bbc", - "when": null, - "workflow_outputs": [] - }, - "22": { - "annotation": "", - "content_id": "wc_gnu", - "errors": null, - "id": 22, - "input_connections": { - "input1": { - "id": 20, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Line/Word/Character count", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 2812.55061813865, - "top": 510.6734558790175 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "wc_gnu", - "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "1.0.0", - "type": "tool", - "uuid": "71d76ee3-7dac-450a-98e9-bb57111df8c5", - "when": null, - "workflow_outputs": [] - }, - "23": { - "annotation": "", - "content_id": "wc_gnu", - "errors": null, - "id": 23, - "input_connections": { - "input1": { - "id": 21, - "output_name": "outfile" - } - }, - "inputs": [], - "label": null, - "name": "Line/Word/Character count", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 3066.1573769206448, - "top": 268.5825615907663 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "wc_gnu", - "tool_state": "{\"include_header\": false, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"options\": [\"lines\"], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "1.0.0", - "type": "tool", - "uuid": "2da84228-d818-493b-bafd-a95959ee2de3", - "when": null, - "workflow_outputs": [] - }, - "24": { - "annotation": "", - "content_id": "param_value_from_file", - "errors": null, - "id": 24, - "input_connections": { - "input1": { - "id": 22, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Parse parameter value", - "outputs": [ - { - "name": "integer_param", - "type": "expression.json" - } - ], - "position": { - "left": 3236.7131866213954, - "top": 502.9407403932288 - }, - "post_job_actions": { - "HideDatasetActioninteger_param": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "integer_param" - } - }, - "tool_id": "param_value_from_file", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "0.1.0", - "type": "tool", - "uuid": "c03bb38c-3383-4d3f-843f-9f74c70b1c47", - "when": null, - "workflow_outputs": [] - }, - "25": { - "annotation": "", - "content_id": "param_value_from_file", - "errors": null, - "id": 25, - "input_connections": { - "input1": { - "id": 23, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Parse parameter value", - "outputs": [ - { - "name": "integer_param", - "type": "expression.json" - } - ], - "position": { - "left": 3349.6578232069623, - "top": 103.77316093552422 - }, - "post_job_actions": { - "HideDatasetActioninteger_param": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "integer_param" - } - }, - "tool_id": "param_value_from_file", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "0.1.0", - "type": "tool", - "uuid": "5ad8559e-e863-45e9-bae2-ede8be8314c7", - "when": null, - "workflow_outputs": [] - }, - "26": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", - "errors": null, - "id": 26, - "input_connections": { - "components_0|param_type|component_value": { - "id": 24, - "output_name": "integer_param" - }, - "components_1|param_type|component_value": { - "id": 25, - "output_name": "integer_param" - } - }, - "inputs": [], - "label": null, - "name": "Calculate numeric parameter value", - "outputs": [ - { - "name": "integer_param", - "type": "expression.json" - } - ], - "position": { - "left": 3600.8912340886463, - "top": 332.9150842713157 - }, - "post_job_actions": { - "HideDatasetActioninteger_param": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "integer_param" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/calculate_numeric_param/calculate_numeric_param/0.1.0", - "tool_shed_repository": { - "changeset_revision": "0e586762f97b", - "name": "calculate_numeric_param", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"-\"}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}, \"arith\": \"\"}], \"output_type\": \"integer\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_uuid": null, - "tool_version": "0.1.0", - "type": "tool", - "uuid": "bdc1a0bf-1614-47f8-90f8-89cc139edf9a", - "when": null, - "workflow_outputs": [] - }, - "27": { + "18": { "annotation": "This step is meant to warn the user that there are duplicated sequence names, which would cause inaccurate alignments results with MashMap. ", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 27, + "id": 18, "input_connections": { "input_param_type|input_param": { - "id": 26, - "output_name": "integer_param" + "id": 16, + "output_name": "Number of Sequences with the same name" + }, + "when": { + "id": 13, + "output_name": "boolean_param" } }, "inputs": [], @@ -3529,8 +5061,8 @@ } ], "position": { - "left": 3822.4432951091107, - "top": 766.5545148192659 + "left": 3399.082051206245, + "top": 120.49976532949609 }, "post_job_actions": { "RenameDatasetActionoutput_param_boolean": { @@ -3553,7 +5085,7 @@ "tool_version": "0.2.0", "type": "tool", "uuid": "4af8e08f-5777-40db-b483-89d68084369b", - "when": null, + "when": "$(inputs.when)", "workflow_outputs": [ { "label": "Fail if there are duplicated sequence names between the fasta files", @@ -3564,7 +5096,7 @@ } }, "tags": [], - "uuid": "62ed4482-aaa8-4942-b327-e16cae8f537f", - "version": 18, - "readme": "# JBrowse2 Precuration Tracks with Related Species Alignments\n\nThis workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species.\n\nThe workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser.\n\n## Inputs\n\n### Required Inputs\n\n1. **Species Name** [text] - Species identifier used in the assembly info report\n2. **Assembly Name** [text] - Assembly identifier (e.g., toLID)\n3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names)\n4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies\n5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes)\n6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`).\n7. **Telomere P** [BED] - P-arm telomere coordinates\n8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty)\n9. **Gaps** [BED] - Assembly gap coordinates\n10. **Coverage** [BigWig] - PacBio HiFi read coverage track\n\n### Gene Annotation Options\n\n11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance\n12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled)\n\n## Outputs\n\n1. **Assembly Info** - Summary of species and assembly name\n2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used)\n3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included\n4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used)\n5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Additional outputs\n\nThese JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view.\n\n6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments\n7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included\n8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments\n9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Validation output\n\n10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas.\n\n## Usage Notes\n\n### Pairing with the Hi-C contact map workflow\n\nThis workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow:\n\n| Hi-C workflow output | Use here as input |\n|---|---|\n| `Decontaminated Hap1 with Suffix` | `Haplotype 1` |\n| `Decontaminated Hap2 with Suffix` | `Haplotype 2` |\n| `P telomeres bed` | `Telomere P` |\n| `Q telomeres Bed` | `Telomere Q` |\n| `Gaps Bed` | `Gaps` |\n| `BigWig Coverage` | `Coverage` |\n| `Compleasm Genes track` | `Genes` |\n\n### Related species selection\n\nChoose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection.\n\n**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example:\n\n```bash\nzcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz\n```\n\n### Scaffold name suffixes\n\nIf using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks.\n\n## Citation\n\nIf you use this workflow, please cite:\n- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z))\n- minimap2 (used for related-species alignment)\n- Other tools as listed in the workflow\n" + "uuid": "e0ef6176-aa34-4385-9df3-04077015cdaa", + "version": 16, + "readme": "# JBrowse2 Precuration Tracks with Related Species Alignments\n\nThis workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species.\n\nThe workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), optionally aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser.\n\n## Inputs\n\nThe workflow auto-detects its operating mode from the data you provide \u2014 there are no toggle parameters to set:\n\n- Provide **Haplotype 2** to switch to dual-haplotype mode (includes hap1-vs-hap2 alignment)\n- Provide **Genes** to add a gene annotation track\n- Provide **Related Species** to add synteny alignments against external genomes\n\nEach of the four combinations produces a different JBrowse2 instance (see Outputs).\n\n### Required inputs\n\n1. **Species Name** [text] - Species identifier used in the assembly info report\n2. **Assembly Name** [text] - Assembly identifier (e.g., toLID)\n3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names)\n4. **Telomere P** [BED] - P-arm telomere coordinates\n5. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty)\n6. **Gaps** [BED] - Assembly gap coordinates\n7. **Coverage** [BigWig] - PacBio HiFi read coverage track\n\n### Optional inputs\n\n8. **Haplotype 2** [fasta] - Secondary haplotype assembly. Provide for diploid assemblies; leave empty for single-haplotype mode.\n9. **Genes** [GFF3] - Gene annotation track. Provide to add a gene track to every JBrowse2 instance.\n10. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`). Leave empty to skip related-species alignment entirely.\n\n## Outputs\n\nThe set of populated outputs depends on which optional inputs are provided. Outputs from inactive modes are present in the history but empty.\n\n### Single-haplotype outputs (Haplotype 2 not provided)\n\n1. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for one haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments\n2. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included (when Genes provided)\n3. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for one haplotype with related-species alignments (when Related Species provided)\n4. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included\n\n### Dual-haplotype outputs (Haplotype 2 provided)\n\n5. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance with hap1-vs-hap2 alignment, no related-species alignments\n6. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included (when Genes provided)\n7. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance with hap1, hap2, and related-species alignments (when Related Species provided)\n8. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included\n\n### Other outputs\n\n9. **Assembly Info** - Summary of species and assembly name\n10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas.\n\n## Usage Notes\n\n### Pairing with the Hi-C contact map workflow\n\nThis workflow is designed to consume the precuration track outputs of the [Hi-C contact map for assembly manual curation](../hi-c-contact-map-for-assembly-manual-curation) workflow:\n\n| Hi-C workflow output | Use here as input |\n|---|---|\n| `Decontaminated Hap1 with Suffix` | `Haplotype 1` |\n| `Decontaminated Hap2 with Suffix` | `Haplotype 2` |\n| `P telomeres bed` | `Telomere P` |\n| `Q telomeres Bed` | `Telomere Q` |\n| `Gaps Bed` | `Gaps` |\n| `BigWig Coverage` | `Coverage` |\n| `Compleasm Genes track` | `Genes` |\n\n### Related species selection\n\nChoose related species whose genomes are evolutionarily close to the assembly under curation, so synteny is informative for spotting misassemblies. Provide them as gzipped FASTA files in a simple list collection.\n\n**Sequence names must be unique across the collection.** The workflow validates this and fails fast if duplicates are detected (e.g. two species both contain `>scaffold_1`). Prefix per-species scaffold names before uploading, for example:\n\n```bash\nzcat Species_1.fasta.gz | sed 's/^>/>Species_1_/' | gzip > Species_1_renamed.fasta.gz\n```\n\n### Scaffold name suffixes\n\nIf using two haplotypes, the recommended workflow is to apply per-haplotype suffixes (e.g. `H1`/`H2`) to scaffold names *before* running this workflow, so that scaffolds from each haplotype are unambiguously identified in the JBrowse view and in synteny tracks.\n\n## Citation\n\nIf you use this workflow, please cite:\n- JBrowse2 ([Diesh et al., 2023](https://doi.org/10.1186/s13059-023-02914-z))\n- minimap2 (used for related-species alignment)\n- Other tools as listed in the workflow\n" } diff --git a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md index d0d3cbf613..e15f8851f0 100644 --- a/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md +++ b/workflows/VGP-assembly-v2/Precuration-Jbrowse-tracks-alignments/README.md @@ -2,47 +2,55 @@ This workflow generates JBrowse2 instances with genome assembly tracks and alignments against related species, to assist the manual curation of genome assemblies. It complements the Hi-C contact map workflow by providing a complementary genome browser view of the same precuration tracks alongside synteny with related species. -The workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser. +The workflow takes the assembly haplotype(s) and the precuration tracks (telomeres, gaps, coverage, optional gene annotations), optionally aligns the assembly against a list of related species, and packages everything into a JBrowse2 instance that curators can open directly in their browser. ## Inputs -### Required Inputs +The workflow auto-detects its operating mode from the data you provide — there are no toggle parameters to set: + +- Provide **Haplotype 2** to switch to dual-haplotype mode (includes hap1-vs-hap2 alignment) +- Provide **Genes** to add a gene annotation track +- Provide **Related Species** to add synteny alignments against external genomes + +Each of the four combinations produces a different JBrowse2 instance (see Outputs). + +### Required inputs 1. **Species Name** [text] - Species identifier used in the assembly info report 2. **Assembly Name** [text] - Assembly identifier (e.g., toLID) 3. **Haplotype 1** [fasta] - Primary haplotype assembly (recommended: with H1 suffix added to scaffold names) -4. **Will you use a second haplotype?** [boolean] - Set to true for diploid assemblies -5. **Haplotype 2** [fasta, optional] - Secondary haplotype assembly (required if using two haplotypes) -6. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`). -7. **Telomere P** [BED] - P-arm telomere coordinates -8. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty) -9. **Gaps** [BED] - Assembly gap coordinates -10. **Coverage** [BigWig] - PacBio HiFi read coverage track +4. **Telomere P** [BED] - P-arm telomere coordinates +5. **Telomere Q** [BED] - Q-arm telomere coordinates (can be empty) +6. **Gaps** [BED] - Assembly gap coordinates +7. **Coverage** [BigWig] - PacBio HiFi read coverage track -### Gene Annotation Options +### Optional inputs -11. **Do you want to provide gene annotation for your assembly?** [boolean] - Enable to include a gene annotation track in the JBrowse2 instance -12. **Genes** [GFF, optional] - Gene annotation track (required if gene annotations enabled) +8. **Haplotype 2** [fasta] - Secondary haplotype assembly. Provide for diploid assemblies; leave empty for single-haplotype mode. +9. **Genes** [GFF3] - Gene annotation track. Provide to add a gene track to every JBrowse2 instance. +10. **Related Species** [collection of fasta.gz] - Simple list of gzipped FASTA files of related species genomes for synteny alignment. **Sequence names must be unique across the entire collection** - the workflow performs a duplicate-name check on the merged related-species fastas and will fail early if any sequence name appears in more than one file. A common pattern is to prefix each species' scaffolds with the species name (e.g. `Species_1_scaffold_1`). Leave empty to skip related-species alignment entirely. ## Outputs -1. **Assembly Info** - Summary of species and assembly name -2. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for a single haplotype with related species alignments (when only one haplotype is used) -3. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included -4. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance for two haplotypes with related species alignments (when two haplotypes are used) -5. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included +The set of populated outputs depends on which optional inputs are provided. Outputs from inactive modes are present in the history but empty. + +### Single-haplotype outputs (Haplotype 2 not provided) -### Additional outputs +1. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for one haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments +2. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included (when Genes provided) +3. **JBrowse2 Single Haplotype with related species** [collection] - JBrowse2 instance for one haplotype with related-species alignments (when Related Species provided) +4. **JBrowse2 Single Haplotype with related species and Gene Tracks** [collection] - As above, with gene annotation tracks included -These JBrowse2 instances are produced without the related-species alignment tracks and can be useful for curators who only need the assembly-internal view. +### Dual-haplotype outputs (Haplotype 2 provided) -6. **JBrowse2 Single Haplotype** [collection] - JBrowse2 instance for a single haplotype with assembly tracks only (telomeres, gaps, coverage), no related-species alignments -7. **JBrowse2 Single Haplotype with Gene Track** [collection] - As above, with gene annotation tracks included -8. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance for two haplotypes with the hap1-vs-hap2 alignment, no related-species alignments -9. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included +5. **JBrowse2 Hap1 vs Hap2** [collection] - JBrowse2 instance with hap1-vs-hap2 alignment, no related-species alignments +6. **JBrowse2 Hap1 vs Hap2 with gene tracks** [collection] - As above, with gene annotation tracks included (when Genes provided) +7. **JBrowse2 Hap1 and hap2 with related species** [collection] - JBrowse2 instance with hap1, hap2, and related-species alignments (when Related Species provided) +8. **JBrowse2 Hap1 and hap2 with related species and gene tracks** [collection] - As above, with gene annotation tracks included -### Validation output +### Other outputs +9. **Assembly Info** - Summary of species and assembly name 10. **Fail if there are duplicated sequence names between the fasta files** [boolean] - Internal validation flag. The workflow fails fast if any sequence name appears in more than one of the related-species fastas. ## Usage Notes