diff --git a/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga b/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga index 876870eaee..b0e6ef414a 100644 --- a/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga +++ b/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga @@ -100,7 +100,6 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1.4", "name": "Allele-based Pathogen Identification", "report": { "markdown": "# Allele-based Pathogen Identification Workflow Report\nBelow are the results for the Allele based Pathogenic Identification Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering), and a FASTA file of the reference genome of the main Pathogen identified in the Gene based Pathogen Identification workflow, or per-known to the user.\n\n## Workflow Output: \n\n### All variants found per sample against the reference genome\n\n```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\")\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"number_of_variants_per_sample\")\n```\n\n### Mapping mean depth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\")\n```\n\n### Mapping breadth of coverage percentage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_coverage_percentage_per_sample\")\n```\n\n" @@ -126,7 +125,7 @@ "top": 205 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", "tool_version": null, "type": "data_collection_input", "uuid": "7aaa03a4-2647-411b-863d-90f28ed01f32", @@ -200,7 +199,7 @@ }, "inputs": [], "label": null, - "name": "Convert compressed file to uncompressed.", + "name": "Convert gz compressed file to uncompressed.", "outputs": [ { "name": "output1", @@ -229,6 +228,7 @@ }, "tool_id": "CONVERTER_gz_to_uncompressed", "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.0", "type": "tool", "uuid": "1ce51556-5526-4c7e-9b94-9634e8e25ed0", @@ -243,7 +243,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy1", "errors": null, "id": 4, "input_connections": { @@ -295,15 +295,16 @@ "output_name": "alignment_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy1", "tool_shed_repository": { - "changeset_revision": "66367287b4e6", + "changeset_revision": "7a6382582d76", "name": "minimap2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"BAM\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"tool_version": "1.15.1+galaxy2", + "tool_uuid": null, + "tool_version": "1.22+galaxy1", "type": "tool", "uuid": "d18e3c23-1d6c-4001-9a77-5167c069585b", "when": null, @@ -450,7 +453,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.22+galaxy3", "errors": null, "id": 7, "input_connections": { @@ -478,15 +481,16 @@ "top": 959.0024861037228 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.22+galaxy3", "tool_shed_repository": { - "changeset_revision": "c4ff13d2aab3", + "changeset_revision": "5160be5d088f", "name": "samtools_coverage", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"additional_options\": {\"min_read_length\": \"0\", \"min_mq\": \"0\", \"min_bq\": \"0\", \"required_flags\": null, \"skipped_flags\": [\"4\", \"256\", \"512\", \"1024\"], \"region\": \"\"}, \"condition_histogram\": {\"histogram_select\": \"no\", \"__current_case__\": 1}, \"condition_input\": {\"input_pooling\": \"No\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"tool_version": "1.15.1+galaxy4", + "tool_state": "{\"atomization\": \"\", \"atomize\": \"false\", \"check_ref\": \"w\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"multiallelics\": {\"mode\": \"\", \"__current_case__\": 0}, \"normalize_indels\": false, \"old_rec_tag\": \"\", \"output_type\": \"v\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rm_dup\": \"\", \"sec_default\": {\"site_win\": \"1000\", \"sort\": \"pos\"}, \"sec_filter_norm\": {\"include\": null, \"exclude\": null}, \"sec_restrict\": {\"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"targets\": {\"targets_src\": \"__none__\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "1.22+galaxy0", "type": "tool", "uuid": "9a34ec91-725e-49b2-973b-1c508e4bdc5d", "when": null, @@ -556,7 +561,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3", "errors": null, "id": 9, "input_connections": { @@ -579,15 +584,16 @@ "top": 623.8951200002152 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "3dc70b59608c", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"delimiter\": \"\", \"colnames_option\": {\"header\": \"N\", \"__current_case__\": 1, \"list\": \"1,2\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.5+galaxy0", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "f6f94754-2660-4fe4-b1dc-937728fc898f", "when": null, @@ -620,6 +626,7 @@ "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.0", "type": "tool", "uuid": "d728f856-b2dd-4261-9b25-84c36bdaced7", @@ -628,7 +635,7 @@ }, "11": { "annotation": "", - 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"tool_version": "1.2.4+galaxy1", + "tool_uuid": null, + "tool_version": "1.2.4+galaxy2", "type": "tool", "uuid": "b20b66f5-e975-4947-8935-8c628d016514", "when": null, @@ -750,6 +759,7 @@ "post_job_actions": {}, "tool_id": "Cut1", "tool_state": "{\"columnList\": \"c6\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.2", "type": "tool", "uuid": "6712cd94-ab45-4052-a2a2-507bbf0652e8", @@ -758,7 +768,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -796,15 +806,16 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0", "tool_shed_repository": { - "changeset_revision": "5fab4f81391d", + "changeset_revision": "0abc5513f795", "name": "snpsift", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"empty_text\": \"\", \"extract\": \"CHROM POS ID REF ALT FILTER\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": false, \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.3+t.galaxy0", + "tool_uuid": null, + "tool_version": "5.4.0c+galaxy0", "type": "tool", "uuid": "c9d51e45-9c09-438e-ab4b-c280a91dd2bc", "when": null, @@ -818,7 +829,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.22+galaxy0", "errors": null, "id": 15, "input_connections": { @@ -834,11 +845,11 @@ "inputs": [ { "description": "runtime parameter for tool bcftools consensus", - "name": "reference_source" + "name": "masking_options" }, { "description": "runtime parameter for tool bcftools consensus", - 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"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "3dc70b59608c", + "changeset_revision": "ab83aa685821", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"complement\": \"\", \"count\": \"1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.5+galaxy0", + "tool_uuid": null, + "tool_version": "9.5+galaxy3", "type": "tool", "uuid": "49b1771c-f107-4dff-8683-65aa58c1c0ad", "when": null, @@ -1249,6 +1269,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"same_once\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "5.1.0", "type": "tool", "uuid": "282932f1-bbc9-4081-b154-ddb3a2ecb779", @@ -1303,6 +1324,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^$\", \"replacement\": \"0\"}], \"field\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.3", "type": "tool", "uuid": "dfa6d815-9c8a-4a04-8862-00a6f83789dc", @@ -1322,6 +1344,7 @@ "name:PathoGFAIR", "name:IWC" ], - "uuid": "435875a1-72c4-4fda-8943-3a78f25c6574", - "version": 72 + "uuid": "db21d0fe-f78b-4e8b-bb19-ec3890883b6d", + "version": 1, + "release": "0.1.5" } \ No newline at end of file diff --git a/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/CHANGELOG.md index f5444486bc..48e81694b8 100644 --- a/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/pathogen-identification/allele-based-pathogen-identification/CHANGELOG.md @@ -1,5 +1,19 @@ # Changelog +## [0.1.5] - 2026-07-06 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.31+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.22+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.22+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.22+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/5.4.0c+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.22+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy3` + ## [0.1.4] - 2025-03-10 ### Automatic update