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Original file line number Diff line number Diff line change
@@ -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

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Original file line number Diff line number Diff line change
Expand Up @@ -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"
},
Expand Down Expand Up @@ -90,7 +89,7 @@
"top": 532.3671875
},
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"tool_version": null,
"type": "data_collection_input",
"uuid": "2864b493-6d12-4313-ad29-f3b1e2564aba",
Expand All @@ -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": {
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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"
}
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