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\"png\", \"qc_output_directory\": \"\", \"report_natural_peptides\": \"false\", \"rt_tolerance_s\": \"30.0\", \"use_averagine_ids\": \"false\", \"use_unassigned_ids\": \"false\", \"weight_merge_window\": \"5.0\", \"xic_threshold\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.6+galaxy0", + "type": "tool", + "uuid": "224b7012-ffd4-4286-9338-97ac411bb313", + "workflow_outputs": [ + { + "label": "Peptide centric result", + "output_name": "out_peptide_centric_csv", + "uuid": "55caf3eb-3c76-45a8-9ff8-55a9dc97e31d" + }, + { + "label": "Feature fitting result", + "output_name": "out_csv", + "uuid": "fb12ff1c-1973-49a2-b5aa-6c1f7127279d" + } + ] + } + }, + "tags": [ + "name:Proteomics" + ], + "uuid": "7046bcc7-f135-486d-b247-21b045a5630b", + "version": 6 +} \ No newline at end of file From 87f53f5b18554ffd8c77a841e1ec145ebf595a2a Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 12 Apr 2023 18:03:51 +0200 Subject: [PATCH 02/12] add tests --- .../openms-metaprosip/.dockstore.yml | 7 + .../openms-metaprosip/metaprosip-tests.yml | 22 ++ .../openms-metaprosip/metaprosip.ga | 354 +++++++++--------- 3 files changed, 199 insertions(+), 184 deletions(-) create mode 100644 workflows/proteomics/openms-metaprosip/.dockstore.yml create mode 100644 workflows/proteomics/openms-metaprosip/metaprosip-tests.yml diff --git a/workflows/proteomics/openms-metaprosip/.dockstore.yml b/workflows/proteomics/openms-metaprosip/.dockstore.yml new file mode 100644 index 000000000..b837c0a54 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/.dockstore.yml @@ -0,0 +1,7 @@ +version: 2.8.0 +workflows: +- name: main + primaryDescriptorPath: /metaprosip.ga + subclass: Galaxy + testParameterFiles: + - /metaprosip-tests.yml diff --git a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml new file mode 100644 index 000000000..c0b0e8960 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml @@ -0,0 +1,22 @@ +- doc: Test outline for MetaProSIP + job: + Fasta Database: + class: File + location: https://abibuilder.cs.uni-tuebingen.de/archive/openms/galaxy-testdata/metaprosip/Zeitz_1and2_454AllContigs_HEX.fasta + filetype: fasta + Centroided LC-MS datasets: + class: Collection + collection_type: list + elements: + - class: File + identifier: Zeitz_SIP_13-II_020_picked.mzML + location: https://abibuilder.cs.uni-tuebingen.de/archive/openms/galaxy-testdata/metaprosip/Zeitz_SIP_13-II_020_picked.mzML + outputs: + Peptide centric result: + element_tests: + Zeitz_SIP_13-II_020_picked.mzML: + path: test-data/Peptide centric result_Zeitz_SIP_13-II_020_picked.mzML.csv + Feature fitting result: + element_tests: + Zeitz_SIP_13-II_020_picked.mzML: + path: test-data/Feature fitting result_Zeitz_SIP_13-II_020_picked.mzML.csv diff --git a/workflows/proteomics/openms-metaprosip/metaprosip.ga b/workflows/proteomics/openms-metaprosip/metaprosip.ga index aa33ba869..71cae55dd 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip.ga +++ b/workflows/proteomics/openms-metaprosip/metaprosip.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "MetaProSIP OpenMS 2.8", + "name": "MetaProSIP OpenMS 2.8 (imported from uploaded file)", "steps": { "0": { "annotation": "", @@ -28,14 +28,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "bottom": 586.3000030517578, - "height": 82.19999694824219, - "left": 320.5, - "right": 520.5, - "top": 504.1000061035156, - "width": 200, - "x": 320.5, - "y": 504.1000061035156 + "left": 0.0, + "top": 131.06323768352638 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -60,14 +54,8 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 1012.9666748046875, - "height": 61.79998779296875, - "left": 320.5, - "right": 520.5, - "top": 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"name": "spectra" @@ -413,38 +400,32 @@ } ], "position": { - "bottom": 984.5333251953125, - "height": 276.4000244140625, - "left": 1706.5, - "right": 1906.5, - "top": 708.13330078125, - "width": 200, - "x": 1706.5, - "y": 708.13330078125 + "left": 1385.9482337688578, + "top": 335.1149460365031 }, - "post_job_actions": { - "HideDatasetActionout": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0", + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "39caaa778d2e", + "changeset_revision": "adca857b4884", "name": "openms_idmapper", "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"consensus\": {\"use_subelements\": \"false\", \"annotate_ids_with_subelements\": \"false\"}, \"feature\": {\"use_centroid_rt\": \"false\", \"use_centroid_mz\": \"true\"}, \"id\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"mz_measure\": \"ppm\", \"mz_reference\": \"peptide\", \"mz_tolerance\": \"20.0\", \"rt_tolerance\": \"5.0\", \"spectra\": {\"_in\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.6+galaxy0", + "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"ignore_charge\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"consensus\": {\"use_subelements\": \"false\", \"annotate_ids_with_subelements\": \"false\"}, \"feature\": {\"use_centroid_rt\": \"false\", \"use_centroid_mz\": \"true\"}, \"id\": {\"__class__\": \"RuntimeValue\"}, \"in\": {\"__class__\": \"RuntimeValue\"}, \"mz_measure\": \"ppm\", \"mz_reference\": \"peptide\", \"mz_tolerance\": \"20.0\", \"rt_tolerance\": \"5.0\", \"spectra\": {\"_in\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "d59740a0-a78e-44d1-9481-b9249e3489b6", - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "out", + "uuid": "9afd6308-0449-4986-b0f6-119a896c290b" + } + ] }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.8+galaxy0", "errors": null, "id": 9, "input_connections": { @@ -461,7 +442,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool MetaProSIP", + "name": "in_fasta" + }, + { + "description": "runtime parameter for tool MetaProSIP", + "name": "in_featureXML" + }, + { + "description": "runtime parameter for tool MetaProSIP", + "name": "in_mzML" + } + ], "label": null, "name": "MetaProSIP", "outputs": [ @@ -475,44 +469,36 @@ } ], "position": { - "bottom": 859.2999725341797, - "height": 225.1999969482422, - "left": 1986.4666748046875, - "right": 2186.4666748046875, - "top": 634.0999755859375, - "width": 200, - "x": 1986.4666748046875, - "y": 634.0999755859375 + "left": 1646.9253013873922, + "top": 597.2701500202047 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.8+galaxy0", "tool_shed_repository": { - "changeset_revision": "41a21bbf40d8", + "changeset_revision": "819ed5aae76f", "name": "openms_metaprosip", "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"cluster\": \"false\", \"correlation_threshold\": \"0.7\", \"decomposition_threshold\": \"0.7\", \"filter_monoisotopic\": \"false\", \"in_fasta\": {\"__class__\": \"ConnectedValue\"}, \"in_featureXML\": {\"__class__\": \"ConnectedValue\"}, \"in_mzML\": {\"__class__\": \"ConnectedValue\"}, \"intensity_threshold\": \"10.0\", \"labeling_element\": \"C\", \"mz_tolerance_ppm\": \"10.0\", \"plot_extension\": \"png\", \"qc_output_directory\": \"\", \"report_natural_peptides\": \"false\", \"rt_tolerance_s\": \"30.0\", \"use_averagine_ids\": \"false\", \"use_unassigned_ids\": \"false\", \"weight_merge_window\": \"5.0\", \"xic_threshold\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.6+galaxy0", + "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"min_correlation_distance_to_averagine\": \"-1.0\", \"pattern_15N_TIC_threshold\": \"0.95\", \"pattern_13C_TIC_threshold\": \"0.95\", \"pattern_2H_TIC_threshold\": \"0.95\", \"pattern_18O_TIC_threshold\": \"0.95\", \"heatmap_bins\": \"20\", \"observed_peak_fraction\": \"0.5\", \"min_consecutive_isotopes\": \"2\", \"score_plot_yaxis_min\": \"0.0\", \"collect_method\": \"correlation_maximum\", \"lowRIA_correlation_threshold\": \"-1.0\", \"force\": \"false\", \"test\": \"False\"}, \"cluster\": \"false\", \"correlation_threshold\": \"0.7\", \"decomposition_threshold\": \"0.7\", \"filter_monoisotopic\": \"false\", \"in_fasta\": {\"__class__\": \"RuntimeValue\"}, \"in_featureXML\": {\"__class__\": \"RuntimeValue\"}, \"in_mzML\": {\"__class__\": \"RuntimeValue\"}, \"intensity_threshold\": \"10.0\", \"labeling_element\": \"C\", \"mz_tolerance_ppm\": \"10.0\", \"plot_extension\": \"png\", \"qc_output_directory\": \"\", \"report_natural_peptides\": \"false\", \"rt_tolerance_s\": \"30.0\", \"use_averagine_ids\": \"false\", \"use_unassigned_ids\": \"false\", \"weight_merge_window\": \"5.0\", \"xic_threshold\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "224b7012-ffd4-4286-9338-97ac411bb313", "workflow_outputs": [ { "label": "Peptide centric result", "output_name": "out_peptide_centric_csv", - "uuid": "55caf3eb-3c76-45a8-9ff8-55a9dc97e31d" + "uuid": "148e023e-c96b-49a9-97ba-b0bc68753966" }, { "label": "Feature fitting result", "output_name": "out_csv", - "uuid": "fb12ff1c-1973-49a2-b5aa-6c1f7127279d" + "uuid": "d312a86c-c659-4405-89c1-2cd661df0c52" } ] } }, - "tags": [ - "name:Proteomics" - ], - "uuid": "7046bcc7-f135-486d-b247-21b045a5630b", - "version": 6 + "tags": [], + "uuid": "f49daca3-3976-4c8c-a2e5-6fc86f2517b4", + "version": 7 } \ No newline at end of file From d92d5474abfbaaff56ec9c747b6c0f03a844d9f7 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 13 Apr 2023 09:36:09 +0200 Subject: [PATCH 03/12] try assetions --- .../openms-metaprosip/metaprosip-tests.yml | 23 +++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml index c0b0e8960..b9e8c7b5e 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml +++ b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml @@ -11,12 +11,31 @@ - class: File identifier: Zeitz_SIP_13-II_020_picked.mzML location: https://abibuilder.cs.uni-tuebingen.de/archive/openms/galaxy-testdata/metaprosip/Zeitz_SIP_13-II_020_picked.mzML + filetype: mzml outputs: Peptide centric result: element_tests: Zeitz_SIP_13-II_020_picked.mzML: - path: test-data/Peptide centric result_Zeitz_SIP_13-II_020_picked.mzML.csv + asserts: + - that: "has_n_columns" + n: 134 + - that: "has_n_lines" + n: 85 + - that: "has_text" + text: "Peptide Sequence" + - that: "has_text" + text: "AATGTPSPAGSPPPIVPAPK" + # path: test-data/Peptide centric result_Zeitz_SIP_13-II_020_picked.mzML.csv Feature fitting result: element_tests: Zeitz_SIP_13-II_020_picked.mzML: - path: test-data/Feature fitting result_Zeitz_SIP_13-II_020_picked.mzML.csv + asserts: + # - that: "has_n_columns" + # n: 134 + - that: "has_n_lines" + n: 4091 + - that: "has_text" + text: "Group 1" + - that: "has_text" + text: "LYSFHTLHQTYMK" + # path: test-data/Feature fitting result_Zeitz_SIP_13-II_020_picked.mzML.csv From e8f03810b49a8c7b7b645466960e822730eae326 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 13 Apr 2023 09:57:38 +0200 Subject: [PATCH 04/12] add README and CHANGELOG --- .../proteomics/openms-metaprosip/CHANGELOG.md | 4 ++++ .../proteomics/openms-metaprosip/README.md | 19 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 workflows/proteomics/openms-metaprosip/CHANGELOG.md create mode 100644 workflows/proteomics/openms-metaprosip/README.md diff --git a/workflows/proteomics/openms-metaprosip/CHANGELOG.md b/workflows/proteomics/openms-metaprosip/CHANGELOG.md new file mode 100644 index 000000000..a023e8e99 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/CHANGELOG.md @@ -0,0 +1,4 @@ +# Changelog + +## [0.1] 2023-04-13 +First release. diff --git a/workflows/proteomics/openms-metaprosip/README.md b/workflows/proteomics/openms-metaprosip/README.md new file mode 100644 index 000000000..570f89255 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/README.md @@ -0,0 +1,19 @@ +# MetaProSIP: automated inference of elemental fluxes in microbial communities + +## Inputs dataset + +- mzML +- Fasta (aminoacid sequences) + +## Inputs values + +## Processing + +- DecoyDatabase: Add decoy sequences to the Fasta database (for FDR calculation) +- FeatureFinderCentroided: identify eluting peptides that correspond to isotopologues with natural isotopic distributions +- MSGFPlusAdapter: identify peptides through peptide fragment fingerprinting (database search) +- FeatureFinderMultiplex +- PeptideIndexer +- FalseDiscoveryRate: Calculate FDR +- IDMapper +- MetaProSIP: calculate the protein-SIP features, to perform functional grouping, and for protein inference From 40e847f001a0cafbe0e8f9afd34edc65876cace2 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 13 Apr 2023 09:58:50 +0200 Subject: [PATCH 05/12] add .workflowhub.yml --- workflows/proteomics/openms-metaprosip/.workflowhub.yml | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 workflows/proteomics/openms-metaprosip/.workflowhub.yml diff --git a/workflows/proteomics/openms-metaprosip/.workflowhub.yml b/workflows/proteomics/openms-metaprosip/.workflowhub.yml new file mode 100644 index 000000000..28b3e2b22 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/.workflowhub.yml @@ -0,0 +1,5 @@ +version: '0.1' +registries: +- url: https://workflowhub.eu + project: iwc + workflow: metaprosip/main From f6f539612b95316dd07966d981d5d407ded5db92 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 13 Apr 2023 09:59:12 +0200 Subject: [PATCH 06/12] update --- workflows/proteomics/openms-metaprosip/.dockstore.yml | 2 +- workflows/proteomics/openms-metaprosip/metaprosip.ga | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/.dockstore.yml b/workflows/proteomics/openms-metaprosip/.dockstore.yml index b837c0a54..0caf9b90f 100644 --- a/workflows/proteomics/openms-metaprosip/.dockstore.yml +++ b/workflows/proteomics/openms-metaprosip/.dockstore.yml @@ -1,4 +1,4 @@ -version: 2.8.0 +version: 0.1 workflows: - name: main primaryDescriptorPath: /metaprosip.ga diff --git a/workflows/proteomics/openms-metaprosip/metaprosip.ga b/workflows/proteomics/openms-metaprosip/metaprosip.ga index 71cae55dd..01f85315a 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip.ga +++ b/workflows/proteomics/openms-metaprosip/metaprosip.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "name": "MetaProSIP OpenMS 2.8 (imported from uploaded file)", + "name": "MetaProSIP OpenMS 2.8", "steps": { "0": { "annotation": "", From dda0e85b36b26e312daa8ad84b620d1e4dfe577c Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 13 Apr 2023 11:33:12 +0200 Subject: [PATCH 07/12] omit column assertion --- workflows/proteomics/openms-metaprosip/metaprosip-tests.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml index b9e8c7b5e..ecd55c05b 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml +++ b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml @@ -17,25 +17,19 @@ element_tests: Zeitz_SIP_13-II_020_picked.mzML: asserts: - - that: "has_n_columns" - n: 134 - that: "has_n_lines" n: 85 - that: "has_text" text: "Peptide Sequence" - that: "has_text" text: "AATGTPSPAGSPPPIVPAPK" - # path: test-data/Peptide centric result_Zeitz_SIP_13-II_020_picked.mzML.csv Feature fitting result: element_tests: Zeitz_SIP_13-II_020_picked.mzML: asserts: - # - that: "has_n_columns" - # n: 134 - that: "has_n_lines" n: 4091 - that: "has_text" text: "Group 1" - that: "has_text" text: "LYSFHTLHQTYMK" - # path: test-data/Feature fitting result_Zeitz_SIP_13-II_020_picked.mzML.csv From 26bb53ab154a70e1b5822f852e24d4cbf99cc467 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 15 May 2023 13:32:37 +0200 Subject: [PATCH 08/12] Apply suggestions from code review Co-authored-by: Timo Sachsenberg --- workflows/proteomics/openms-metaprosip/README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/README.md b/workflows/proteomics/openms-metaprosip/README.md index 570f89255..883c014d4 100644 --- a/workflows/proteomics/openms-metaprosip/README.md +++ b/workflows/proteomics/openms-metaprosip/README.md @@ -12,8 +12,8 @@ - DecoyDatabase: Add decoy sequences to the Fasta database (for FDR calculation) - FeatureFinderCentroided: identify eluting peptides that correspond to isotopologues with natural isotopic distributions - MSGFPlusAdapter: identify peptides through peptide fragment fingerprinting (database search) -- FeatureFinderMultiplex -- PeptideIndexer +- FeatureFinderMultiplex: detect elution profiles of unlabeled peptides +- PeptideIndexer: annotate protein association to identified peptides - FalseDiscoveryRate: Calculate FDR -- IDMapper +- IDMapper: map identified spectra to elution profiles - MetaProSIP: calculate the protein-SIP features, to perform functional grouping, and for protein inference From 98e9792156438695e4a01ec75cf8ff49a6c6dc4b Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 1 Jun 2023 20:58:40 +0200 Subject: [PATCH 09/12] add some workflow parameters --- .../openms-metaprosip/metaprosip-tests.yml | 4 + .../openms-metaprosip/metaprosip.ga | 282 +++++++++++++----- 2 files changed, 205 insertions(+), 81 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml index ecd55c05b..4849d7a02 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml +++ b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml @@ -12,6 +12,10 @@ identifier: Zeitz_SIP_13-II_020_picked.mzML location: https://abibuilder.cs.uni-tuebingen.de/archive/openms/galaxy-testdata/metaprosip/Zeitz_SIP_13-II_020_picked.mzML filetype: mzml + Precursor monoisotopic mass tolerance (ppm): '10.0' + Fixed modifications: Carbamidomethyl (C) + Variable modifications: Oxidation (M) + Labeled element: C outputs: Peptide centric result: element_tests: diff --git a/workflows/proteomics/openms-metaprosip/metaprosip.ga b/workflows/proteomics/openms-metaprosip/metaprosip.ga index 01f85315a..34dc0e548 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip.ga +++ b/workflows/proteomics/openms-metaprosip/metaprosip.ga @@ -13,14 +13,14 @@ "name": "MetaProSIP OpenMS 2.8", "steps": { "0": { - "annotation": "", + "annotation": "mgf, ms2, mzml or mzxml datasets", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "", + "description": "mgf, ms2, mzml or mzxml datasets", "name": "Centroided LC-MS datasets" } ], @@ -28,8 +28,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, - "top": 131.06323768352638 + "left": 7.076599011515327, + "top": 131.0592459605027 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -39,14 +39,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "", + "annotation": "A protein sequence database in FASTA format", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "", + "description": "A protein sequence database in FASTA format", "name": "Fasta Database" } ], @@ -54,8 +54,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, - "top": 578.1321558459051 + "left": 5.760014806230345, + "top": 248.23459645790086 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -65,17 +65,126 @@ "workflow_outputs": [] }, "2": { + "annotation": "passed to\n\n- MSGF+ -precursor_mass_tolerance\n- MetaProSIP -mz_tolerance_ppm", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "passed to\n\n- MSGF+ -precursor_mass_tolerance\n- MetaProSIP -mz_tolerance_ppm", + "name": "Precursor monoisotopic mass tolerance (ppm)" + } + ], + "label": "Precursor monoisotopic mass tolerance (ppm)", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 9.126262562065165, + "top": 663.2704811849542 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"float\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "f5dd354c-a6af-490a-9613-93f269eefebe", + "workflow_outputs": [] + }, + "3": { + "annotation": "used for the MSGF+ search", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, + "inputs": [ + { + "description": "used for the MSGF+ search", + "name": "Fixed modifications" + } + ], + "label": "Fixed modifications", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 10.008971181763343, + "top": 804.5182698932969 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "f1d7a7ce-4007-456b-aa64-e673391ca563", + "workflow_outputs": [] + }, + "4": { + "annotation": "used for the MSGF+ search", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "used for the MSGF+ search", + "name": "Variable modifications" + } + ], + "label": "Variable modifications", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 6.208847840341662, + "top": 930.8498115471064 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, 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"output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort collection", + "name": "input" + } + ], "label": null, "name": "Sort collection", "outputs": [ @@ -85,28 +194,28 @@ } ], "position": { - "left": 275.976983432112, - "top": 115.05747827990297 + "left": 283.10891498997137, + "top": 115.05087230963167 + }, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } }, - "post_job_actions": {}, "tool_id": "__SORTLIST__", - "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": 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"variable_modifications": { + "id": 4, + "output_name": "output" } }, "inputs": [ @@ -233,8 +354,8 @@ } ], "position": { - "left": 555.9195682920257, - "top": 293.1321768925107 + "left": 563.0759987411635, + "top": 293.11789986903193 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.8+galaxy0", @@ -244,7 +365,7 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"PeptideIndexing\": {\"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"missing_decoy_action\": \"warn\", \"write_protein_sequence\": \"false\", \"write_protein_description\": \"false\", \"keep_unreferenced_proteins\": \"false\", \"unmatched_action\": \"error\", \"aaa_max\": \"3\", \"mismatches_max\": \"0\", \"IL_equivalent\": \"false\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}}, \"add_features\": \"true\", \"adv_opts\": {\"add_decoys\": \"false\", 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\"decoy_string_position\": \"prefix\", \"missing_decoy_action\": \"warn\", \"write_protein_sequence\": \"false\", \"write_protein_description\": \"false\", \"keep_unreferenced_proteins\": \"false\", \"unmatched_action\": \"error\", \"aaa_max\": \"3\", \"mismatches_max\": \"0\", \"IL_equivalent\": \"false\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}}, \"add_features\": \"true\", \"adv_opts\": {\"add_decoys\": \"false\", \"legacy_conversion\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"conf\": {\"__class__\": \"RuntimeValue\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"enzyme\": \"Trypsin/P\", \"fixed_modifications\": {\"__class__\": \"ConnectedValue\"}, \"fragment_method\": \"from_spectrum\", \"in\": {\"__class__\": \"RuntimeValue\"}, \"instrument\": \"low_res\", \"isotope_error_range\": \"0,1\", \"matches_per_spec\": \"1\", \"max_missed_cleavages\": \"-1\", \"max_mods\": \"2\", \"max_peptide_length\": \"40\", \"max_precursor_charge\": \"3\", \"min_peptide_length\": \"6\", \"min_precursor_charge\": \"2\", \"precursor_error_units\": \"ppm\", \"precursor_mass_tolerance\": {\"__class__\": \"ConnectedValue\"}, \"protocol\": \"automatic\", \"reindex\": \"true\", \"tasks\": \"0\", \"tryptic\": \"fully\", \"variable_modifications\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "4edeb1a3-bc6e-44d0-8633-1bc439ca988e", @@ -252,35 +373,26 @@ { "label": null, "output_name": "out", - "uuid": "cc53806b-3b10-4a24-9c8d-a316b14e2bd0" + "uuid": "2c144632-b584-4866-ab3f-12e7b84a3533" } ] }, - "6": { + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.8+galaxy0", "errors": null, - "id": 6, + "id": 10, "input_connections": { "fasta": { - "id": 3, + "id": 7, "output_name": "out" }, "in": { - "id": 5, + "id": 9, "output_name": "out" } }, - "inputs": [ - { - "description": "runtime parameter for tool PeptideIndexer", - "name": "fasta" - }, - { - "description": "runtime parameter for tool PeptideIndexer", - "name": "in" - } - ], + "inputs": [], "label": null, "name": "PeptideIndexer", "outputs": [ @@ -290,8 +402,8 @@ } ], "position": { - "left": 833.9942669046335, - "top": 522.2701500202047 + "left": 856.0592678761781, + "top": 468.58170130950543 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.8+galaxy0", @@ -301,7 +413,7 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"IL_equivalent\": \"false\", \"OPTIONAL_OUTPUTS\": null, \"aaa_max\": \"3\", \"adv_opts\": {\"force\": \"false\", \"test\": \"False\"}, \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"in\": {\"__class__\": \"RuntimeValue\"}, \"keep_unreferenced_proteins\": \"false\", \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": \"false\", \"write_protein_sequence\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"IL_equivalent\": \"false\", \"OPTIONAL_OUTPUTS\": null, \"aaa_max\": \"3\", \"adv_opts\": {\"force\": \"false\", \"test\": \"False\"}, \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"keep_unreferenced_proteins\": \"false\", \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": \"false\", \"write_protein_sequence\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "87a572fe-0b20-478e-bbc3-58b1dff8bc7d", @@ -309,18 +421,18 @@ { "label": null, "output_name": "out", - "uuid": "04d8e0c8-f9af-42bf-bc16-87e14408d0ca" + "uuid": "79b9f9dd-906f-4e9c-919d-c76f639f99bf" } ] }, - "7": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.8+galaxy0", "errors": null, - "id": 7, + "id": 11, "input_connections": { "in": { - "id": 6, + "id": 10, "output_name": "out" } }, @@ -339,8 +451,8 @@ } ], "position": { - "left": 1138.5344406654094, - "top": 739.4252382475754 + "left": 1145.676234466169, + "top": 739.3926076015834 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.8+galaxy0", @@ -358,22 +470,22 @@ { "label": null, "output_name": "out", - "uuid": "3be6a8dc-61d4-4230-baf9-eef29a38e42b" + "uuid": "61530731-cce2-470c-8c97-1f0800f124c9" } ] }, - "8": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.8+galaxy0", "errors": null, - "id": 8, + "id": 12, "input_connections": { "id": { - "id": 7, + "id": 11, "output_name": "out" }, "in": { - "id": 4, + "id": 8, "output_name": "out" } }, @@ -400,8 +512,8 @@ } ], "position": { - "left": 1385.9482337688578, - "top": 335.1149460365031 + "left": 1393.1927501192213, + "top": 335.08378855843944 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.8+galaxy0", @@ -419,25 +531,33 @@ { "label": null, "output_name": "out", - "uuid": "9afd6308-0449-4986-b0f6-119a896c290b" + "uuid": "7f1e1091-6958-4fdb-887c-c04e7e7f3679" } ] }, - "9": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.8+galaxy0", "errors": null, - "id": 9, + "id": 13, "input_connections": { "in_fasta": { - "id": 3, + "id": 7, "output_name": "out" }, "in_featureXML": { - "id": 8, + "id": 12, "output_name": "out" }, "in_mzML": { + "id": 6, + "output_name": "output" + }, + "labeling_element": { + "id": 5, + "output_name": "output" + }, + "mz_tolerance_ppm": { "id": 2, "output_name": "output" } @@ -469,8 +589,8 @@ } ], "position": { - "left": 1646.9253013873922, - "top": 597.2701500202047 + "left": 1666.1430646529957, + "top": 604.6828127849037 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.8+galaxy0", @@ -480,7 +600,7 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"min_correlation_distance_to_averagine\": \"-1.0\", \"pattern_15N_TIC_threshold\": \"0.95\", \"pattern_13C_TIC_threshold\": \"0.95\", \"pattern_2H_TIC_threshold\": \"0.95\", \"pattern_18O_TIC_threshold\": \"0.95\", \"heatmap_bins\": \"20\", \"observed_peak_fraction\": \"0.5\", \"min_consecutive_isotopes\": \"2\", \"score_plot_yaxis_min\": \"0.0\", \"collect_method\": \"correlation_maximum\", \"lowRIA_correlation_threshold\": \"-1.0\", \"force\": \"false\", \"test\": \"False\"}, \"cluster\": \"false\", \"correlation_threshold\": \"0.7\", \"decomposition_threshold\": \"0.7\", \"filter_monoisotopic\": \"false\", \"in_fasta\": {\"__class__\": \"RuntimeValue\"}, \"in_featureXML\": {\"__class__\": \"RuntimeValue\"}, \"in_mzML\": {\"__class__\": \"RuntimeValue\"}, \"intensity_threshold\": \"10.0\", \"labeling_element\": \"C\", \"mz_tolerance_ppm\": \"10.0\", \"plot_extension\": \"png\", \"qc_output_directory\": \"\", \"report_natural_peptides\": \"false\", \"rt_tolerance_s\": \"30.0\", \"use_averagine_ids\": \"false\", \"use_unassigned_ids\": \"false\", \"weight_merge_window\": \"5.0\", \"xic_threshold\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"min_correlation_distance_to_averagine\": \"-1.0\", \"pattern_15N_TIC_threshold\": \"0.95\", \"pattern_13C_TIC_threshold\": \"0.95\", \"pattern_2H_TIC_threshold\": \"0.95\", \"pattern_18O_TIC_threshold\": \"0.95\", \"heatmap_bins\": \"20\", \"observed_peak_fraction\": \"0.5\", \"min_consecutive_isotopes\": \"2\", \"score_plot_yaxis_min\": \"0.0\", \"collect_method\": \"correlation_maximum\", \"lowRIA_correlation_threshold\": \"-1.0\", \"force\": \"false\", \"test\": \"False\"}, \"cluster\": \"false\", \"correlation_threshold\": \"0.7\", \"decomposition_threshold\": \"0.7\", \"filter_monoisotopic\": \"false\", \"in_fasta\": {\"__class__\": \"RuntimeValue\"}, \"in_featureXML\": {\"__class__\": \"RuntimeValue\"}, \"in_mzML\": {\"__class__\": \"RuntimeValue\"}, \"intensity_threshold\": \"10.0\", \"labeling_element\": {\"__class__\": \"ConnectedValue\"}, \"mz_tolerance_ppm\": {\"__class__\": \"ConnectedValue\"}, \"plot_extension\": \"png\", \"qc_output_directory\": \"\", \"report_natural_peptides\": \"false\", \"rt_tolerance_s\": \"30.0\", \"use_averagine_ids\": \"false\", \"use_unassigned_ids\": \"false\", \"weight_merge_window\": \"5.0\", \"xic_threshold\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "224b7012-ffd4-4286-9338-97ac411bb313", @@ -488,17 +608,17 @@ { "label": "Peptide centric result", "output_name": "out_peptide_centric_csv", - "uuid": "148e023e-c96b-49a9-97ba-b0bc68753966" + "uuid": "1985589f-e690-48e4-a41f-7dc20eb7446f" }, { "label": "Feature fitting result", "output_name": "out_csv", - "uuid": "d312a86c-c659-4405-89c1-2cd661df0c52" + "uuid": "b2370639-8c23-46a6-be8a-b2136d0b8de0" } ] } }, "tags": [], - "uuid": "f49daca3-3976-4c8c-a2e5-6fc86f2517b4", - "version": 7 -} \ No newline at end of file + "uuid": "79e1d2ac-7d1a-49ba-b7f6-c8f66f0bdef5", + "version": 6 +} From 313cd8f1ce1280f9d8d74a2bf42e978ec57b03bd Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 14 Sep 2023 15:10:07 +0200 Subject: [PATCH 10/12] update readme --- workflows/proteomics/openms-metaprosip/README.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/README.md b/workflows/proteomics/openms-metaprosip/README.md index 883c014d4..d0bb6c82c 100644 --- a/workflows/proteomics/openms-metaprosip/README.md +++ b/workflows/proteomics/openms-metaprosip/README.md @@ -2,11 +2,18 @@ ## Inputs dataset -- mzML -- Fasta (aminoacid sequences) +- `Centroided LC-MS datasets` in mzML (MetaProSIP is mainly tested on data generated by orbitrap instruments) +- `Fasta Database` in Fasta (aminoacid sequences) ## Inputs values +- `Precursor monoisotopic mass tolerance` (ppm): This value is passed to + - MSGFPlusAdapter parameter `Precursor monoisotopic mass tolerance` (-precursor_mass_tolerance) + - MetaProSIP parameter `Tolerance in ppm` (-mz_tolerance_ppm) +- Fixed modifications +- Variable modifications +- Labeled element + ## Processing - DecoyDatabase: Add decoy sequences to the Fasta database (for FDR calculation) From 6348d2d7049ccdc4167c2c6e2883f1fdec427012 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Thu, 14 Sep 2023 21:02:26 +0200 Subject: [PATCH 11/12] Apply suggestions from code review Co-authored-by: Marius van den Beek --- .../openms-metaprosip/.dockstore.yml | 5 ++++- .../openms-metaprosip/metaprosip-tests.yml | 22 +++++++++---------- .../openms-metaprosip/metaprosip.ga | 1 + 3 files changed, 16 insertions(+), 12 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/.dockstore.yml b/workflows/proteomics/openms-metaprosip/.dockstore.yml index 0caf9b90f..a6407d1d1 100644 --- a/workflows/proteomics/openms-metaprosip/.dockstore.yml +++ b/workflows/proteomics/openms-metaprosip/.dockstore.yml @@ -1,7 +1,10 @@ -version: 0.1 +version: 1.2 workflows: - name: main primaryDescriptorPath: /metaprosip.ga subclass: Galaxy testParameterFiles: - /metaprosip-tests.yml + authors: + - name: Matthias Bernt + orcid: 0000-0003-3763-0797 diff --git a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml index 4849d7a02..d3be8fe73 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml +++ b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml @@ -12,7 +12,7 @@ identifier: Zeitz_SIP_13-II_020_picked.mzML location: https://abibuilder.cs.uni-tuebingen.de/archive/openms/galaxy-testdata/metaprosip/Zeitz_SIP_13-II_020_picked.mzML filetype: mzml - Precursor monoisotopic mass tolerance (ppm): '10.0' + Precursor monoisotopic mass tolerance (ppm): 10.0 Fixed modifications: Carbamidomethyl (C) Variable modifications: Oxidation (M) Labeled element: C @@ -21,19 +21,19 @@ element_tests: Zeitz_SIP_13-II_020_picked.mzML: asserts: - - that: "has_n_lines" + - that: has_n_lines n: 85 - - that: "has_text" - text: "Peptide Sequence" - - that: "has_text" - text: "AATGTPSPAGSPPPIVPAPK" + - that: has_text + text: Peptide Sequence + - that: has_text + text: AATGTPSPAGSPPPIVPAPK Feature fitting result: element_tests: Zeitz_SIP_13-II_020_picked.mzML: asserts: - - that: "has_n_lines" + - that: has_n_lines n: 4091 - - that: "has_text" - text: "Group 1" - - that: "has_text" - text: "LYSFHTLHQTYMK" + - that: has_text + text: Group 1 + - that: has_text + text: LYSFHTLHQTYMK diff --git a/workflows/proteomics/openms-metaprosip/metaprosip.ga b/workflows/proteomics/openms-metaprosip/metaprosip.ga index 34dc0e548..8ad878a29 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip.ga +++ b/workflows/proteomics/openms-metaprosip/metaprosip.ga @@ -9,6 +9,7 @@ } ], "format-version": "0.1", + "release": "0.1", "license": "MIT", "name": "MetaProSIP OpenMS 2.8", "steps": { From f5790ce7191886b45ced70be928113cecbd5d01c Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 15 Sep 2023 15:31:26 +0200 Subject: [PATCH 12/12] only the MetaProSIP outputs should be workflow outputs --- .../openms-metaprosip/metaprosip.ga | 177 ++++++------------ 1 file changed, 55 insertions(+), 122 deletions(-) diff --git a/workflows/proteomics/openms-metaprosip/metaprosip.ga b/workflows/proteomics/openms-metaprosip/metaprosip.ga index 8ad878a29..288268ccb 100644 --- a/workflows/proteomics/openms-metaprosip/metaprosip.ga +++ b/workflows/proteomics/openms-metaprosip/metaprosip.ga @@ -9,7 +9,6 @@ } ], "format-version": "0.1", - "release": "0.1", "license": "MIT", "name": "MetaProSIP OpenMS 2.8", "steps": { @@ -30,13 +29,14 @@ "outputs": [], "position": { "left": 7.076599011515327, - "top": 131.0592459605027 + "top": 129.1847085591696 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "7676403b-b391-41fe-b07b-a35a13ff318f", + "when": null, "workflow_outputs": [] }, "1": { @@ -56,13 +56,14 @@ "outputs": [], "position": { "left": 5.760014806230345, - "top": 248.23459645790086 + "top": 246.36005905656776 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "27f8d0f6-773b-4373-ad0a-b3b1ddb0b6ec", + "when": null, "workflow_outputs": [] }, "2": { @@ -82,13 +83,14 @@ "outputs": [], "position": { "left": 9.126262562065165, - "top": 663.2704811849542 + "top": 661.3959437836211 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"float\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "f5dd354c-a6af-490a-9613-93f269eefebe", + "when": null, "workflow_outputs": [] }, "3": { @@ -108,13 +110,14 @@ "outputs": [], "position": { "left": 10.008971181763343, - "top": 804.5182698932969 + "top": 802.6437324919638 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "f1d7a7ce-4007-456b-aa64-e673391ca563", + "when": null, "workflow_outputs": [] }, "4": { @@ -134,13 +137,14 @@ "outputs": [], "position": { "left": 6.208847840341662, - "top": 930.8498115471064 + "top": 928.9752741457733 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "b3ef07df-9879-4b2d-860a-6395606f7c25", + "when": null, "workflow_outputs": [] }, "5": { @@ -159,14 +163,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 0.0, - "top": 1055.1765619959394 + "left": 0, + "top": 1053.3020245946063 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "65dc4bdd-aff3-4e04-8420-3f49d44fbcb9", + "when": null, "workflow_outputs": [] }, "6": { @@ -180,12 +185,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Sort collection", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Sort collection", "outputs": [ @@ -196,7 +196,7 @@ ], "position": { "left": 283.10891498997137, - "top": 115.05087230963167 + "top": 113.17633490829857 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -206,10 +206,11 @@ } }, "tool_id": "__SORTLIST__", - "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "428ef215-857a-4525-a650-240c1b1a4d85", + "when": null, "workflow_outputs": [] }, "7": { @@ -233,8 +234,8 @@ } ], "position": { - "left": 259.8593556046271, - "top": 445.1675688985006 + "left": 259.8666687011719, + "top": 444.29214961038565 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.8+galaxy0", @@ -244,17 +245,12 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"Decoy\": {\"non_shuffle_pattern\": \"\", \"keepPeptideNTerm\": \"true\", \"keepPeptideCTerm\": \"true\"}, \"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"shuffle_max_attempts\": \"30\", \"shuffle_sequence_identity_threshold\": \"0.5\", \"seed\": \"1\", \"force\": \"false\", \"test\": \"False\"}, \"decoy_string\": \"DECOY_\", \"decoy_string_position\": \"prefix\", \"enzyme\": \"Trypsin\", \"in_cond\": {\"in_select\": \"no\", \"__current_case__\": 0, \"in\": {\"__class__\": \"ConnectedValue\"}}, \"method\": \"reverse\", \"only_decoy\": \"false\", \"type\": \"protein\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"Decoy\": {\"non_shuffle_pattern\": \"\", \"keepPeptideNTerm\": true, \"keepPeptideCTerm\": true}, \"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"shuffle_max_attempts\": \"30\", \"shuffle_sequence_identity_threshold\": \"0.5\", \"seed\": \"1\", \"force\": false, \"test\": \"False\"}, \"decoy_string\": \"DECOY_\", \"decoy_string_position\": \"prefix\", \"enzyme\": \"Trypsin\", \"in_cond\": {\"in_select\": \"no\", \"__current_case__\": 0, \"in\": {\"__class__\": \"ConnectedValue\"}}, \"method\": \"reverse\", \"only_decoy\": false, \"type\": \"protein\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "dbe2ad39-3591-46c8-abf1-2fcbe284f78e", - "workflow_outputs": [ - { - "label": null, - "output_name": "out", - "uuid": "afb43a4b-c998-431a-974d-28b59752f3ea" - } - ] + "when": null, + "workflow_outputs": [] }, "8": { "annotation": "", @@ -267,12 +263,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool FeatureFinderMultiplex", - "name": "in" - } - ], + "inputs": [], "label": null, "name": "FeatureFinderMultiplex", "outputs": [ @@ -282,7 +273,7 @@ } ], "position": { - "left": 889.0933682289328, + "left": 889.1042176446133, "top": 0.0 }, "post_job_actions": {}, @@ -293,17 +284,12 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"adv_opts\": {\"force\": \"false\", \"test\": \"False\"}, \"algorithm\": {\"labels\": \"\", \"charge\": \"1:4\", \"isotopes_per_peptide\": \"3:6\", \"rt_typical\": \"40.0\", \"rt_band\": \"0.0\", \"rt_min\": \"2.0\", \"mz_tolerance\": \"6.0\", \"mz_unit\": \"ppm\", \"intensity_cutoff\": \"1000.0\", \"peptide_similarity\": \"0.5\", \"averagine_similarity\": \"0.4\", \"averagine_similarity_scaling\": \"0.95\", \"missed_cleavages\": \"0\", \"spectrum_type\": \"automatic\", \"averagine_type\": \"peptide\", \"knock_out\": \"false\"}, \"in\": {\"__class__\": \"RuntimeValue\"}, \"labels\": {\"Arg6\": \"6.0201290268\", \"Arg10\": \"10.0082686\", \"Lys4\": \"4.0251069836\", \"Lys6\": \"6.0201290268\", \"Lys8\": \"8.0141988132\", \"Leu3\": \"3.01883\", \"Dimethyl0\": \"28.0313\", \"Dimethyl4\": \"32.056407\", \"Dimethyl6\": \"34.063117\", \"Dimethyl8\": \"36.07567\", \"ICPL0\": \"105.021464\", \"ICPL4\": \"109.046571\", \"ICPL6\": \"111.041593\", \"ICPL10\": \"115.0667\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"adv_opts\": {\"force\": false, \"test\": \"False\"}, \"algorithm\": {\"labels\": \"\", \"charge\": \"1:4\", \"isotopes_per_peptide\": \"3:6\", \"rt_typical\": \"40.0\", \"rt_band\": \"0.0\", \"rt_min\": \"2.0\", \"mz_tolerance\": \"6.0\", \"mz_unit\": \"ppm\", \"intensity_cutoff\": \"1000.0\", \"peptide_similarity\": \"0.5\", \"averagine_similarity\": \"0.4\", \"averagine_similarity_scaling\": \"0.95\", \"missed_cleavages\": \"0\", \"spectrum_type\": \"automatic\", \"averagine_type\": \"peptide\", \"knock_out\": false}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"labels\": {\"Arg6\": \"6.0201290268\", \"Arg10\": \"10.0082686\", \"Lys4\": \"4.0251069836\", \"Lys6\": \"6.0201290268\", \"Lys8\": \"8.0141988132\", \"Leu3\": \"3.01883\", \"Dimethyl0\": \"28.0313\", \"Dimethyl4\": \"32.056407\", \"Dimethyl6\": \"34.063117\", \"Dimethyl8\": \"36.07567\", \"ICPL0\": \"105.021464\", \"ICPL4\": \"109.046571\", \"ICPL6\": \"111.041593\", \"ICPL10\": \"115.0667\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "a98005bb-1181-4632-939c-520962481b41", - "workflow_outputs": [ - { - "label": null, - "output_name": "out", - "uuid": "166a695e-e033-4c1b-8b4e-8b2f1cf2e800" - } - ] + "when": null, + "workflow_outputs": [] }, "9": { "annotation": "", @@ -336,14 +322,6 @@ { "description": "runtime parameter for tool MSGFPlusAdapter", "name": "conf" - }, - { - "description": "runtime parameter for tool MSGFPlusAdapter", - "name": "database" - }, - { - "description": "runtime parameter for tool MSGFPlusAdapter", - "name": "in" } ], "label": null, @@ -356,7 +334,7 @@ ], "position": { "left": 563.0759987411635, - "top": 293.11789986903193 + "top": 291.24336246769883 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.8+galaxy0", @@ -366,17 +344,12 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"PeptideIndexing\": {\"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"missing_decoy_action\": \"warn\", \"write_protein_sequence\": \"false\", \"write_protein_description\": \"false\", \"keep_unreferenced_proteins\": \"false\", \"unmatched_action\": \"error\", \"aaa_max\": \"3\", \"mismatches_max\": \"0\", \"IL_equivalent\": \"false\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}}, \"add_features\": \"true\", \"adv_opts\": {\"add_decoys\": \"false\", \"legacy_conversion\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"conf\": {\"__class__\": \"RuntimeValue\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"enzyme\": \"Trypsin/P\", \"fixed_modifications\": {\"__class__\": \"ConnectedValue\"}, \"fragment_method\": \"from_spectrum\", \"in\": {\"__class__\": \"RuntimeValue\"}, \"instrument\": \"low_res\", \"isotope_error_range\": \"0,1\", \"matches_per_spec\": \"1\", \"max_missed_cleavages\": \"-1\", \"max_mods\": \"2\", \"max_peptide_length\": \"40\", \"max_precursor_charge\": \"3\", \"min_peptide_length\": \"6\", \"min_precursor_charge\": \"2\", \"precursor_error_units\": \"ppm\", \"precursor_mass_tolerance\": {\"__class__\": \"ConnectedValue\"}, \"protocol\": \"automatic\", \"reindex\": \"true\", \"tasks\": \"0\", \"tryptic\": \"fully\", \"variable_modifications\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"PeptideIndexing\": {\"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"missing_decoy_action\": \"warn\", \"write_protein_sequence\": false, \"write_protein_description\": false, \"keep_unreferenced_proteins\": false, \"unmatched_action\": \"error\", \"aaa_max\": \"3\", \"mismatches_max\": \"0\", \"IL_equivalent\": false, \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}}, \"add_features\": true, \"adv_opts\": {\"add_decoys\": false, \"legacy_conversion\": false, \"force\": false, \"test\": \"False\"}, \"conf\": {\"__class__\": \"RuntimeValue\"}, \"database\": {\"__class__\": \"ConnectedValue\"}, \"enzyme\": \"Trypsin/P\", \"fixed_modifications\": {\"__class__\": \"ConnectedValue\"}, \"fragment_method\": \"from_spectrum\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"instrument\": \"low_res\", \"isotope_error_range\": \"0,1\", \"matches_per_spec\": \"1\", \"max_missed_cleavages\": \"-1\", \"max_mods\": \"2\", \"max_peptide_length\": \"40\", \"max_precursor_charge\": \"3\", \"min_peptide_length\": \"6\", \"min_precursor_charge\": \"2\", \"precursor_error_units\": \"ppm\", \"precursor_mass_tolerance\": {\"__class__\": \"ConnectedValue\"}, \"protocol\": \"automatic\", \"reindex\": true, \"tasks\": \"0\", \"tryptic\": \"fully\", \"variable_modifications\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "4edeb1a3-bc6e-44d0-8633-1bc439ca988e", - "workflow_outputs": [ - { - "label": null, - "output_name": "out", - "uuid": "2c144632-b584-4866-ab3f-12e7b84a3533" - } - ] + "when": null, + "workflow_outputs": [] }, "10": { "annotation": "", @@ -404,7 +377,7 @@ ], "position": { "left": 856.0592678761781, - "top": 468.58170130950543 + "top": 466.70716390817233 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.8+galaxy0", @@ -414,17 +387,12 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"IL_equivalent\": \"false\", \"OPTIONAL_OUTPUTS\": null, \"aaa_max\": \"3\", \"adv_opts\": {\"force\": \"false\", \"test\": \"False\"}, \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"keep_unreferenced_proteins\": \"false\", \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": \"false\", \"write_protein_sequence\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"IL_equivalent\": false, \"OPTIONAL_OUTPUTS\": null, \"aaa_max\": \"3\", \"adv_opts\": {\"force\": false, \"test\": \"False\"}, \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"auto\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"keep_unreferenced_proteins\": false, \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": false, \"write_protein_sequence\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "87a572fe-0b20-478e-bbc3-58b1dff8bc7d", - "workflow_outputs": [ - { - "label": null, - "output_name": "out", - "uuid": "79b9f9dd-906f-4e9c-919d-c76f639f99bf" - } - ] + "when": null, + "workflow_outputs": [] }, "11": { "annotation": "", @@ -437,12 +405,7 @@ "output_name": "out" } }, - "inputs": [ - { - "description": "runtime parameter for tool FalseDiscoveryRate", - "name": "in" - } - ], + "inputs": [], "label": null, "name": "FalseDiscoveryRate", "outputs": [ @@ -453,7 +416,7 @@ ], "position": { "left": 1145.676234466169, - "top": 739.3926076015834 + "top": 737.5180702002503 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.8+galaxy0", @@ -463,17 +426,12 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"FDR\": {\"PSM\": \"1.0\", \"protein\": \"1.0\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"true\", \"adv_opts\": {\"force\": \"false\", \"test\": \"False\"}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"false\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"in\": {\"__class__\": \"RuntimeValue\"}, \"protein\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"FDR\": {\"PSM\": \"1.0\", \"protein\": \"1.0\", \"cleanup\": {\"remove_proteins_without_psms\": true, \"remove_psms_without_proteins\": true, \"remove_spectra_without_psms\": true}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": true, \"adv_opts\": {\"force\": false, \"test\": \"False\"}, \"algorithm\": {\"no_qvalues\": false, \"use_all_hits\": false, \"split_charge_variants\": false, \"treat_runs_separately\": false, \"add_decoy_peptides\": false, \"add_decoy_proteins\": false, \"conservative\": true}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "21e5233c-0395-44aa-814a-e690c9a759db", - "workflow_outputs": [ - { - "label": null, - "output_name": "out", - "uuid": "61530731-cce2-470c-8c97-1f0800f124c9" - } - ] + "when": null, + "workflow_outputs": [] }, "12": { "annotation": "", @@ -491,14 +449,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool IDMapper", - "name": "id" - }, - { - "description": "runtime parameter for tool IDMapper", - "name": "in" - }, { "description": "runtime parameter for tool IDMapper", "name": "spectra" @@ -514,7 +464,7 @@ ], "position": { "left": 1393.1927501192213, - "top": 335.08378855843944 + "top": 333.20925115710634 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.8+galaxy0", @@ -524,17 +474,12 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"ignore_charge\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"consensus\": {\"use_subelements\": \"false\", \"annotate_ids_with_subelements\": \"false\"}, \"feature\": {\"use_centroid_rt\": \"false\", \"use_centroid_mz\": \"true\"}, \"id\": {\"__class__\": \"RuntimeValue\"}, \"in\": {\"__class__\": \"RuntimeValue\"}, \"mz_measure\": \"ppm\", \"mz_reference\": \"peptide\", \"mz_tolerance\": \"20.0\", \"rt_tolerance\": \"5.0\", \"spectra\": {\"_in\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"ignore_charge\": false, \"force\": false, \"test\": \"False\"}, \"consensus\": {\"use_subelements\": false, \"annotate_ids_with_subelements\": false}, \"feature\": {\"use_centroid_rt\": false, \"use_centroid_mz\": true}, \"id\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"mz_measure\": \"ppm\", \"mz_reference\": \"peptide\", \"mz_tolerance\": \"20.0\", \"rt_tolerance\": \"5.0\", \"spectra\": {\"_in\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "d59740a0-a78e-44d1-9481-b9249e3489b6", - "workflow_outputs": [ - { - "label": null, - "output_name": "out", - "uuid": "7f1e1091-6958-4fdb-887c-c04e7e7f3679" - } - ] + "when": null, + "workflow_outputs": [] }, "13": { "annotation": "", @@ -563,20 +508,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool MetaProSIP", - "name": "in_fasta" - }, - { - "description": "runtime parameter for tool MetaProSIP", - "name": "in_featureXML" - }, - { - "description": "runtime parameter for tool MetaProSIP", - "name": "in_mzML" - } - ], + "inputs": [], "label": null, "name": "MetaProSIP", "outputs": [ @@ -591,7 +523,7 @@ ], "position": { "left": 1666.1430646529957, - "top": 604.6828127849037 + "top": 602.8082753835706 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.8+galaxy0", @@ -601,25 +533,26 @@ "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"min_correlation_distance_to_averagine\": \"-1.0\", \"pattern_15N_TIC_threshold\": \"0.95\", \"pattern_13C_TIC_threshold\": \"0.95\", \"pattern_2H_TIC_threshold\": \"0.95\", \"pattern_18O_TIC_threshold\": \"0.95\", \"heatmap_bins\": \"20\", \"observed_peak_fraction\": \"0.5\", \"min_consecutive_isotopes\": \"2\", \"score_plot_yaxis_min\": \"0.0\", \"collect_method\": \"correlation_maximum\", \"lowRIA_correlation_threshold\": \"-1.0\", \"force\": \"false\", \"test\": \"False\"}, \"cluster\": \"false\", \"correlation_threshold\": \"0.7\", \"decomposition_threshold\": \"0.7\", \"filter_monoisotopic\": \"false\", \"in_fasta\": {\"__class__\": \"RuntimeValue\"}, \"in_featureXML\": {\"__class__\": \"RuntimeValue\"}, \"in_mzML\": {\"__class__\": \"RuntimeValue\"}, \"intensity_threshold\": \"10.0\", \"labeling_element\": {\"__class__\": \"ConnectedValue\"}, \"mz_tolerance_ppm\": {\"__class__\": \"ConnectedValue\"}, \"plot_extension\": \"png\", \"qc_output_directory\": \"\", \"report_natural_peptides\": \"false\", \"rt_tolerance_s\": \"30.0\", \"use_averagine_ids\": \"false\", \"use_unassigned_ids\": \"false\", \"weight_merge_window\": \"5.0\", \"xic_threshold\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts\": {\"min_correlation_distance_to_averagine\": \"-1.0\", \"pattern_15N_TIC_threshold\": \"0.95\", \"pattern_13C_TIC_threshold\": \"0.95\", \"pattern_2H_TIC_threshold\": \"0.95\", \"pattern_18O_TIC_threshold\": 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\"__rerun_remap_job_id__\": null}", "tool_version": "2.8+galaxy0", "type": "tool", "uuid": "224b7012-ffd4-4286-9338-97ac411bb313", + "when": null, "workflow_outputs": [ - { - "label": "Peptide centric result", - "output_name": "out_peptide_centric_csv", - "uuid": "1985589f-e690-48e4-a41f-7dc20eb7446f" - }, { "label": "Feature fitting result", "output_name": "out_csv", "uuid": "b2370639-8c23-46a6-be8a-b2136d0b8de0" + }, + { + "label": "Peptide centric result", + "output_name": "out_peptide_centric_csv", + "uuid": "1985589f-e690-48e4-a41f-7dc20eb7446f" } ] } }, "tags": [], - "uuid": "79e1d2ac-7d1a-49ba-b7f6-c8f66f0bdef5", - "version": 6 + "uuid": "b03da1a7-fc6f-419f-aa2c-431a670f9a96", + "version": 1 }