From 035be2bf54340d48debda31472af6bc90c17ccce Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 6 Jul 2026 09:42:24 +0000 Subject: [PATCH] Updating workflows/metabolomics/gcms-metams from 0.2 to 0.3 --- .../metabolomics/gcms-metams/CHANGELOG.md | 5 +++++ .../Mass-spectrometry__GCMS-with-metaMS.ga | 21 ++++++++++++------- 2 files changed, 19 insertions(+), 7 deletions(-) diff --git a/workflows/metabolomics/gcms-metams/CHANGELOG.md b/workflows/metabolomics/gcms-metams/CHANGELOG.md index 88dcb50833..8221f0cbfc 100644 --- a/workflows/metabolomics/gcms-metams/CHANGELOG.md +++ b/workflows/metabolomics/gcms-metams/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.3] - 2026-07-06 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0` was updated to `toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/4.0.0+galaxy0` + ## [0.2] - 2025-05-05 ### Automatic update diff --git a/workflows/metabolomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga b/workflows/metabolomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga index d90acda80e..608ea7ab2d 100644 --- a/workflows/metabolomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga +++ b/workflows/metabolomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS.ga @@ -34,7 +34,7 @@ "top": 101 }, "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": "27aea272-13ef-4ab2-81ef-329830985fe0", @@ -101,6 +101,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "2.16.1+galaxy3", "type": "tool", "uuid": "60192f76-c4a8-4505-a24e-e730fe87694e", @@ -148,6 +149,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"file_load_section\": {\"file_load_conditional\": {\"file_load_select\": \"no\", \"__current_case__\": 0}}, \"filterSection\": {\"filterAcquisitionNum\": \"\", \"filterRt\": \"\", \"filterMz\": \"\"}, \"image\": {\"__class__\": \"ConnectedValue\"}, \"methods\": {\"method\": \"MatchedFilter\", \"__current_case__\": 1, \"fwhm\": \"5\", \"binSize\": \"0.5\", \"MatchedFilterAdv\": {\"impute_cond\": {\"impute\": \"none\", \"__current_case__\": 0}, \"sigma\": null, \"max\": \"500\", \"snthresh\": \"2\", \"steps\": \"2\", \"mzdiff\": \"0.5\", \"peaklist\": false}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "3.12.0+galaxy3", "type": "tool", "uuid": "117244c7-a9b0-4143-bfba-48c6cca56ee5", @@ -195,6 +197,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"rdata.xcms.findchrompeaks\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"file_load_section\": {\"file_load_conditional\": {\"file_load_select\": \"no\", \"__current_case__\": 0}}, \"images\": {\"__class__\": \"ConnectedValue\"}, \"sampleMetadata\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "3.12.0+galaxy3", "type": "tool", "uuid": "a5e5e89e-4521-49b4-9554-1004cefb3842", @@ -249,6 +252,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"rdata.xcms.findchrompeaks\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"file_load_section\": {\"file_load_conditional\": {\"file_load_select\": \"no\", \"__current_case__\": 0}}, \"images\": {\"__class__\": \"ConnectedValue\"}, \"sampleMetadata\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "3.12.0+galaxy3", "type": "tool", "uuid": "cb2b0664-f992-4e0b-8a40-58c83a0e47f9", @@ -308,6 +312,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"options_rifilter\": {\"option\": \"false\", \"__current_case__\": 1}, \"settings\": {\"setting\": \"usersettings\", \"__current_case__\": 1, \"options_rtrange\": {\"option\": \"hide\", \"__current_case__\": 1}, \"rtdiff\": \"0.05\", \"minfeat\": \"5\", \"simthreshold\": \"0.7\", \"minclassfraction\": \"0.5\", \"minclasssize\": \"3\", \"options_db\": {\"option\": \"hide\", \"__current_case__\": 1}, \"options_ri\": {\"option\": \"hide\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "3.0.0+metaMS1.24.0-galaxy0", "type": "tool", "uuid": "4f636be8-c31f-474e-8c47-8fd644710863", @@ -327,7 +332,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/4.0.0+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -370,15 +375,16 @@ "top": 281 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/4.0.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "e7c5811ec12f", + "changeset_revision": "f19a3307db9b", "name": "checkformat", "owner": "ethevenot", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"dataMatrix_in\": {\"__class__\": \"ConnectedValue\"}, \"makeNameL\": \"FALSE\", \"sampleMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"variableMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.0.0", + "tool_uuid": null, + "tool_version": "4.0.0+galaxy0", "type": "tool", "uuid": "a3701788-b7fd-4eb9-adf1-d3834a935567", "when": null, @@ -437,6 +443,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advCpt\": {\"opcC\": \"full\", \"__current_case__\": 1, \"scaleC\": \"standard\", \"permI\": \"20\", \"log10L\": \"FALSE\", \"algoC\": \"default\", \"crossvalI\": \"3\"}, \"advGph\": {\"opgC\": \"full\", \"__current_case__\": 1, \"typeC\": \"summary\", \"parMahalC\": \"NA\", \"parAsColC\": \"class\", \"parLabVc\": \"none\", \"parPc1I\": \"1\", \"parPc2I\": \"2\", \"parCexN\": \"0.8\"}, \"dataMatrix_in\": {\"__class__\": \"ConnectedValue\"}, \"orthoI\": \"0\", \"predI\": \"NA\", \"respC\": \"none\", \"sampleMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"save_rdata\": false, \"testL\": \"FALSE\", \"variableMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_uuid": null, "tool_version": "2.3.10", "type": "tool", "uuid": "52e89249-a543-441c-8da6-60b7e40178b2", @@ -463,7 +470,7 @@ "GTN", "metaMS" ], - "uuid": "7abd10fb-d083-4732-b11f-56581e23905d", + "uuid": "aad5b57f-a526-4f3f-910a-c9ee9bb92839", "version": 1, - "release": "0.2" + "release": "0.3" } \ No newline at end of file