From 4a595e1a3d39102704cd6e2dc1d9a26e6702a3e9 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 6 Apr 2026 08:13:39 +0000 Subject: [PATCH] Updating workflows/proteomics/clinicalmp/clinicalmp-quantitation from 0.1 to 0.2 --- .../clinicalmp-quantitation/CHANGELOG.md | 5 ++++ .../iwc-clinicalmp-quantitation.ga | 27 ++++++++++++------- 2 files changed, 22 insertions(+), 10 deletions(-) diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/CHANGELOG.md b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/CHANGELOG.md index 7850ec41e2..4d457aeb77 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/CHANGELOG.md +++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2] - 2026-04-06 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy2` + ## [0.1] - 2024-08-14 diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga index 9021d3f8aa..1ce79bde45 100644 --- a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga +++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation.ga @@ -11,7 +11,6 @@ "format-version": "0.1", "license": "CC-BY-4.0", "name": "Clinical Metaproteomics Quantitation", - "release": "0.1", "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" }, @@ -90,7 +89,7 @@ "top": 532.3671875 }, "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": "2864b493-6d12-4313-ad29-f3b1e2564aba", @@ -99,7 +98,7 @@ }, "3": { "annotation": "Database searching", - "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy2", "errors": null, "id": 3, "input_connections": { @@ -155,15 +154,16 @@ "top": 170.17578125 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy2", "tool_shed_repository": { - "changeset_revision": "9c52362ae7bb", + "changeset_revision": "022e886e8f94", "name": "maxquant", "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": false, \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\", \"msms\", \"evidence\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"reporter_ion_ms2\", \"__current_case__\": 3, \"iso_labels\": {\"labeling\": \"tmt11plex\", \"__current_case__\": 4}, \"filter_by_pif\": {\"filter_pif\": \"False\", \"__current_case__\": 1}}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": true}, \"lfq_opts\": {\"separateLfq\": false, \"lfqStabilizeLargeRatios\": true, \"lfqRequireMsms\": true, \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": true}}, \"qc\": {\"do_it\": \"false\", \"__current_case__\": 1}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"8\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"0\", \"calc_peak_properties\": false, \"mbr\": {\"match_between_runs\": \"True\", \"__current_case__\": 1, \"matching_time_window\": \"0.7\", \"matching_ion_mobility_window\": \"0.05\", \"alignment_time_window\": \"20\", \"alignment_ion_mobility_window\": \"1\", \"match_unidentified_features\": false}, \"incl_contaminants\": false, \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"50\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0.3.0+galaxy0", + "tool_state": "{\"input_opts\": {\"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": false, \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\", \"msms\", \"evidence\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"reporter_ion_ms2\", \"__current_case__\": 3, \"iso_labels\": {\"labeling\": \"tmt11plex\", \"__current_case__\": 4}, \"filter_by_pif\": {\"filter_pif\": \"False\", \"__current_case__\": 1}}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": true}, \"lfq_opts\": {\"separateLfq\": false, \"lfqStabilizeLargeRatios\": true, \"lfqRequireMsms\": true, \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": true}}, \"qc\": {\"__current_case__\": 1, \"do_it\": \"false\"}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"8\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"0\", \"calc_peak_properties\": false, \"mbr\": {\"match_between_runs\": \"True\", \"__current_case__\": 1, \"matching_time_window\": \"0.7\", \"matching_ion_mobility_window\": \"0.05\", \"alignment_time_window\": \"20\", \"alignment_ion_mobility_window\": \"1\", \"match_unidentified_features\": false}, \"incl_contaminants\": false, \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"50\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, + "tool_version": "2.0.3.0+galaxy2", "type": "tool", "uuid": "7e8ec7d9-8fe8-4cf0-a2b3-6358b96c7af5", "when": null, @@ -196,6 +196,7 @@ "post_job_actions": {}, "tool_id": "Grep1", "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"keep_header\": false, \"pattern\": \"(_HUMAN)|(_REVERSED)|(CON)|(con)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.4", "type": "tool", "uuid": "ee371998-9bf4-4462-abad-63d6a73b995e", @@ -229,6 +230,7 @@ "post_job_actions": {}, "tool_id": "Grep1", "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"keep_header\": false, \"pattern\": \"(_HUMAN)|(_REVERSED)|(CON)|(con)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.4", "type": "tool", "uuid": "72ea8f91-5de4-43bc-a2c9-264491627eb2", @@ -262,6 +264,7 @@ "post_job_actions": {}, "tool_id": "Cut1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.2", "type": "tool", "uuid": "44654f5d-e388-4604-bd61-8eda7bd71152", @@ -295,6 +298,7 @@ "post_job_actions": {}, "tool_id": "Cut1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "1.0.2", "type": "tool", "uuid": "c8cc87cd-13ec-418a-8f95-d0d23dd37e6c", @@ -336,6 +340,7 @@ }, "tool_id": "Grouping1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "2.1.4", "type": "tool", "uuid": "d76c6369-3878-45de-9b28-45ae510ba481", @@ -383,6 +388,7 @@ }, "tool_id": "Grouping1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "2.1.4", "type": "tool", "uuid": "019fe847-4fb9-441f-9450-505f855434e7", @@ -399,6 +405,7 @@ "tags": [ "name:clinicalMP" ], - "uuid": "e21d954c-bb46-46f3-8081-0095b6b0de1f", - "version": 1 -} + "uuid": "4d8ddd43-940f-4c32-a5f3-e9f5d403b141", + "version": 1, + "release": "0.2" +} \ No newline at end of file