From 28b09909cbee997b80c383d35e5d8f4e12a9b386 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 15 Jun 2026 10:06:44 +0000 Subject: [PATCH] Updating workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0 from 0.2.2 to 0.2.3 --- .../Mitogenome-assembly-VGP0/CHANGELOG.md | 5 ++ .../Mitogenome-Assembly-VGP0.ga | 59 ++++++++++++++----- 2 files changed, 48 insertions(+), 16 deletions(-) diff --git a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/CHANGELOG.md b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/CHANGELOG.md index 74e7c3ca6d..48a1c38c05 100644 --- a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2.3] - 2026-06-15 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy2` + ## [0.2.2] - 2025-08-25 ### Changes diff --git a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0.ga b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0.ga index 3bb5dc9550..2ea4c1f066 100644 --- a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0.ga +++ b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0.ga @@ -15,7 +15,6 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.2", "name": "Mitogenome Assembly VGP0", "report": { "markdown": "Species : \n\n```galaxy\nhistory_dataset_embedded(output=\"Species Name for report\")\n```\n\nAssembly:\n\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Name for report\")\n```\n\n\n## Annotation\n\n```galaxy\nhistory_dataset_as_image(output=\"Mitogenome annotation: Image\")\n```\n\n## Coverage\n\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Mitogenome coverage: Image\")\n```\r\n\n\n## Contigs Stats\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Mitogenome: Contigs Statistics\")\n```\n" @@ -107,7 +106,7 @@ "top": 369.7578125 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}", + "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", "tool_version": null, "type": "data_collection_input", "uuid": "861c3a49-1055-4030-9a91-e53cbf1ac436", @@ -219,6 +218,7 @@ "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\"}}}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "0.1.1", "type": "tool", "uuid": "d4355c6d-cbbf-4066-9ea6-5257a7555996", @@ -270,6 +270,7 @@ "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\"}}}], \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "0.1.1", "type": "tool", "uuid": "57a0ad31-8816-471a-877b-f495443c8c89", @@ -284,7 +285,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy2", "errors": null, "id": 7, "input_connections": { @@ -297,7 +298,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MitoHiFi", + "name": "operation_mode" + }, + { + "description": "runtime parameter for tool MitoHiFi", + "name": "operation_mode" + } + ], "label": null, "name": "MitoHiFi", "outputs": [ @@ -315,15 +325,16 @@ "top": 589.6796875 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "bfab6f5b449d", + "changeset_revision": "2853471f753d", "name": "mitohifi", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_mode\": {\"command\": \"find_reference\", \"__current_case__\": 0, \"species\": {\"__class__\": \"ConnectedValue\"}, \"email\": {\"__class__\": \"ConnectedValue\"}, \"min_length\": \"15000\", \"exact_species\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.2.3+galaxy0", + "tool_state": "{\"operation_mode\": {\"command\": \"find_reference\", \"__current_case__\": 0, \"species\": {\"__class__\": \"ConnectedValue\"}, \"email\": {\"__class__\": \"ConnectedValue\"}, \"organelle_type\": \"mitochondrion\", \"ncbi_api_key\": \"\", \"min_length\": \"15000\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.2.3+galaxy2", "type": "tool", "uuid": "e59aea2d-9bc3-4e2e-9af2-711f0cdea373", "when": null, @@ -331,7 +342,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy2", "errors": null, "id": 8, "input_connections": { @@ -352,7 +363,20 @@ "output_name": "genbank_reference" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MitoHiFi", + "name": "operation_mode" + }, + { + "description": "runtime parameter for tool MitoHiFi", + "name": "operation_mode" + }, + { + "description": "runtime parameter for tool MitoHiFi", + "name": "operation_mode" + } + ], "label": null, "name": "MitoHiFi", "outputs": [ @@ -471,15 +495,16 @@ "output_name": "mitogenome_genbank" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "bfab6f5b449d", + "changeset_revision": "2853471f753d", "name": "mitohifi", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_mode\": {\"command\": \"mitohifi\", \"__current_case__\": 1, \"input_option\": {\"input\": \"pacbio\", \"__current_case__\": 0, \"input_reads\": {\"__class__\": \"RuntimeValue\"}, \"bloom_filter\": \"0\"}, \"reference_fasta\": {\"__class__\": \"RuntimeValue\"}, \"reference_genbank\": {\"__class__\": \"RuntimeValue\"}, \"organism_selection\": \"animal\", \"genetic_code\": {\"__class__\": \"ConnectedValue\"}, \"advanced_options\": {\"query_blast\": \"70\", \"circular_size\": null, \"circular_offset\": null, \"outputs\": null}, \"output_zip\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.2.3+galaxy0", + "tool_state": "{\"operation_mode\": {\"command\": \"mitohifi\", \"__current_case__\": 1, \"input_option\": {\"input\": \"pacbio\", \"__current_case__\": 0, \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"bloom_filter\": \"0\"}, \"reference_fasta\": {\"__class__\": \"ConnectedValue\"}, \"reference_genbank\": {\"__class__\": \"ConnectedValue\"}, \"organism_selection\": \"animal\", \"genetic_code\": {\"__class__\": \"ConnectedValue\"}, \"advanced_options\": {\"query_blast\": \"70\", \"circular_size\": null, \"circular_offset\": null, \"outputs\": null}, \"output_zip\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "3.2.3+galaxy2", "type": "tool", "uuid": "ccd83410-608a-4b9d-a43a-11cecd6c2d42", "when": null, @@ -554,6 +579,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "0.1.0", "type": "tool", "uuid": "5207adc9-f36a-42e9-8631-e01da77ac446", @@ -571,6 +597,7 @@ "Reviewed", "VGP" ], - "uuid": "7de562f8-2ef4-4277-a88b-c0d12f22f0b6", - "version": 1 + "uuid": "15e111b8-e41a-46a3-b8c7-a52802703c23", + "version": 1, + "release": "0.2.3" } \ No newline at end of file