From 088067a9005dd4945ca5b90daf2a39db02c2dcb1 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Tue, 21 Nov 2023 14:51:36 +0100 Subject: [PATCH 01/15] Add metabomics-lcms-preprocessing WF --- .../GTN_LCMSpreprocessing.ga | 596 +++++ .../GTN_LCMSpreprocessing_tests.yml | 65 + ...llChromPeaks.annotate.variableMetadata.tsv | 2231 +++++++++++++++++ ...e.groupChromPeaks.fillpeaks.dataMatrix.tsv | 2231 +++++++++++++++++ 4 files changed, 5123 insertions(+) create mode 100644 workflows/metabomics-lcms-preprocessing/GTN_LCMSpreprocessing.ga create mode 100644 workflows/metabomics-lcms-preprocessing/GTN_LCMSpreprocessing_tests.yml create mode 100644 workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv create mode 100644 workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv diff --git 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mzml + - class: File + identifier: HU_neg_048.mzML + location: https://zenodo.org/record/10130758/files/HU_neg_048.mzML + filetype: mzml + - class: File + identifier: HU_neg_090.mzML + location: https://zenodo.org/record/10130758/files/HU_neg_090.mzML + filetype: mzml + - class: File + identifier: HU_neg_123.mzML + location: https://zenodo.org/record/10130758/files/HU_neg_123.mzML + filetype: mzml + - class: File + identifier: HU_neg_157.mzML + location: https://zenodo.org/record/10130758/files/HU_neg_157.mzML + filetype: mzml + - class: File + identifier: HU_neg_173.mzML + location: https://zenodo.org/record/10130758/files/HU_neg_173.mzML + filetype: mzml + - class: File + identifier: HU_neg_192.mzML + location: https://zenodo.org/record/10130758/files/HU_neg_192.mzML + filetype: mzml + - class: File + identifier: QC1_002.mzML + location: https://zenodo.org/record/10130758/files/QC1_002.mzML + filetype: mzml + - class: File + identifier: QC1_008.mzML + location: https://zenodo.org/record/10130758/files/QC1_008.mzML + filetype: mzml + - class: File + identifier: QC1_014.mzML + location: https://zenodo.org/record/10130758/files/QC1_014.mzML + filetype: mzml + outputs: + xcms fillChromPeaks dataMatrix: + file: test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv + CAMERA.annotate variableMetadata: + file: test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv + diff --git a/workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv b/workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv new file mode 100644 index 000000000..571c886e0 --- /dev/null +++ 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67589.3798801576 55456.7517846677 30480.8208100778 +M541T700 0 0 0 0 0 0 0 0 0 244908.95258622 193174.240041812 89392.5228204704 +M542T444 0 0 0 384389.105192284 375486.166789256 297647.271267779 218519.398352355 32577.795274149 305228.469419259 312422.512086637 279779.30909757 163161.158711137 +M543T444 0 0 0 4811.15235463395 10708.6760044834 50860.1425277118 24454.0613687697 0 39179.0056759551 47092.9950795791 42828.0016620849 34842.4987829673 +M549T1004 89224.8763961456 76048.2488970164 61890.0852045625 96071.1131658414 102809.946657897 77927.9032414559 71659.171606397 76488.223823659 46027.7128706061 89644.7039411693 62984.0230566292 58696.4122719511 +M564T670 0 0 0 0 0 0 0 0 0 290122.392815463 210008.627913867 94887.1544915947 +M565T1004 81172.8988529492 113761.009505785 87545.7473139174 45165.7686833999 125015.721060389 114116.192653435 106098.370992573 108852.3513039 83943.8368706796 73167.9809890775 94993.8034359073 72023.7170317337 +M566T715 0 0 0 0 0 0 0 0 0 88065.0582933198 81803.6345588375 46505.2344383036 +M589T414 0 0 0 60363.5800195673 0 8994.8200657926 3626.09769707609 0 38533.8286666784 81008.1160507833 93718.60827957 61076.2161042304 +M600T412 0 0 0 99913.7658776567 449955.037337945 282055.958005409 228655.298140211 2456.437581306 385534.145066514 218878.000418846 212706.676555752 122582.593880939 +M663T495 0 0 0 0 110788.268738473 1991610.46161383 108224.210439286 0 13107.8891270362 336194.287429022 440293.768772579 302557.488994999 From 75c0c421bb72d0d7cf7b263c91a745826ce36d65 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Tue, 21 Nov 2023 16:41:43 +0100 Subject: [PATCH 02/15] Add metabomics-lcms-preprocessing WF - remname and add metadata --- ...N_LCMSpreprocessing.ga => LC-MS_preprocessing.ga} | 12 +++++++----- ...essing_tests.yml => LC-MS_preprocessing_test.yml} | 0 2 files changed, 7 insertions(+), 5 deletions(-) rename workflows/metabomics-lcms-preprocessing/{GTN_LCMSpreprocessing.ga => LC-MS_preprocessing.ga} (97%) rename workflows/metabomics-lcms-preprocessing/{GTN_LCMSpreprocessing_tests.yml => LC-MS_preprocessing_test.yml} (100%) diff --git a/workflows/metabomics-lcms-preprocessing/GTN_LCMSpreprocessing.ga b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga similarity index 97% rename from workflows/metabomics-lcms-preprocessing/GTN_LCMSpreprocessing.ga rename to workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga index 43ba8ebec..7378bae38 100644 --- a/workflows/metabomics-lcms-preprocessing/GTN_LCMSpreprocessing.ga +++ b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga @@ -4,12 +4,14 @@ "creator": [ { "class": "Organization", - "name": "workflow4metabolomics" + "image": "https://raw.githubusercontent.com/workflow4metabolomics/workflow4metabolomics/master/images/logo/logo_w4m-0.1-black-orange.png", + "name": "workflow4metabolomics", + "url": "https://workflow4metabolomics.org/" } ], "format-version": "0.1", "license": "MIT", - "name": "GTN_LCMSpreprocessing", + "name": "LC-MS preprocessing", "steps": { "0": { "annotation": "", @@ -375,7 +377,7 @@ "owner": "melpetera", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/shared/mfs/data/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"dataMatrix_in\": {\"__class__\": \"ConnectedValue\"}, \"method_cond\": {\"method\": \"each_class\", \"__current_case__\": 1, \"class_col\": \"2\", \"chosen_stat\": [\"NA\"], \"test_fold_cond\": {\"test_fold\": \"No\", \"__current_case__\": 1}}, \"sampleMetadata_in\": null, \"variableMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/shared/mfs/data/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"dataMatrix_in\": {\"__class__\": \"ConnectedValue\"}, \"method_cond\": {\"method\": \"each_class\", \"__current_case__\": 1, \"class_col\": \"2\", \"chosen_stat\": [\"NA\"], \"test_fold_cond\": {\"test_fold\": \"No\", \"__current_case__\": 1}}, \"sampleMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"variableMetadata_in\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.2.8", "type": "tool", "uuid": "fcbec34b-b0d1-4d09-9873-a3c9c95399dc", @@ -591,6 +593,6 @@ "xcms", "GTN" ], - "uuid": "e2c25b2b-4031-470e-8f84-83307e9ecd98", - "version": 1 + "uuid": "7680429c-e77a-4134-8f4d-90f145e0ca6f", + "version": 2 } \ No newline at end of file diff --git a/workflows/metabomics-lcms-preprocessing/GTN_LCMSpreprocessing_tests.yml b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing_test.yml similarity index 100% rename from workflows/metabomics-lcms-preprocessing/GTN_LCMSpreprocessing_tests.yml rename to workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing_test.yml From ccaa400508a30d0b741989f138781f2b5d7632e8 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Tue, 21 Nov 2023 17:35:57 +0100 Subject: [PATCH 03/15] Add metabomics-lcms-preprocessing WF - follow recommendation --- workflows/metabomics-lcms-preprocessing/.dockstore.yml | 10 ++++++++++ .../LC-MS_preprocessing.ga | 3 ++- 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 workflows/metabomics-lcms-preprocessing/.dockstore.yml diff --git a/workflows/metabomics-lcms-preprocessing/.dockstore.yml b/workflows/metabomics-lcms-preprocessing/.dockstore.yml new file mode 100644 index 000000000..a3ce533f2 --- /dev/null +++ b/workflows/metabomics-lcms-preprocessing/.dockstore.yml @@ -0,0 +1,10 @@ +version: 1.2 +workflows: +- name: main + subclass: Galaxy + publish: true + primaryDescriptorPath: /LC-MS_preprocessing.ga + authors: + - name: workflow4metabolomics + image: https://raw.githubusercontent.com/workflow4metabolomics/workflow4metabolomics/master/images/logo/logo_w4m-0.1-black-orange.png + url: https://workflow4metabolomics.org/ diff --git a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga index 7378bae38..a15b33bae 100644 --- a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga +++ b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga @@ -11,6 +11,7 @@ ], "format-version": "0.1", "license": "MIT", + "release": "0.1", "name": "LC-MS preprocessing", "steps": { "0": { @@ -595,4 +596,4 @@ ], "uuid": "7680429c-e77a-4134-8f4d-90f145e0ca6f", "version": 2 -} \ No newline at end of file +} From 67c282dbadc1e118d4d87a5bfcac0c468b491968 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Wed, 22 Nov 2023 10:02:54 +0100 Subject: [PATCH 04/15] Add metabomics-lcms-preprocessing WF - add docs --- .../CHANGELOG.md | 8 ++++ ..._test.yml => LC-MS_preprocessing-test.yml} | 4 +- .../LC-MS_preprocessing.ga | 4 +- .../metabomics-lcms-preprocessing/README.md | 38 +++++++++++++++++++ 4 files changed, 50 insertions(+), 4 deletions(-) create mode 100644 workflows/metabomics-lcms-preprocessing/CHANGELOG.md rename workflows/metabomics-lcms-preprocessing/{LC-MS_preprocessing_test.yml => LC-MS_preprocessing-test.yml} (96%) create mode 100644 workflows/metabomics-lcms-preprocessing/README.md diff --git a/workflows/metabomics-lcms-preprocessing/CHANGELOG.md b/workflows/metabomics-lcms-preprocessing/CHANGELOG.md new file mode 100644 index 000000000..90622474c --- /dev/null +++ b/workflows/metabomics-lcms-preprocessing/CHANGELOG.md @@ -0,0 +1,8 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +## [0.1] - 2023-11-22 + +First release + diff --git a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing_test.yml b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing-test.yml similarity index 96% rename from workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing_test.yml rename to workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing-test.yml index e2dcc6574..bdcb300f3 100644 --- a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing_test.yml +++ b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing-test.yml @@ -1,11 +1,11 @@ -- doc: Test outline for GTN_LCMSpreprocessing +- doc: Test outline for LC-MS_preprocessing job: SampleMetadata: class: File identifier: sampleMetadata.tsv location: https://zenodo.org/records/10130758/files/sampleMetadata_12samp_completed.tsv filetype: tabular - Chromatagrams Dataset Collection: + Mass-spectrometry Dataset Collection: class: Collection collection_type: list elements: diff --git a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga index a15b33bae..1dfe261b5 100644 --- a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga +++ b/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga @@ -50,10 +50,10 @@ "inputs": [ { "description": "", - "name": "Chromatagrams Dataset Collection" + "name": "Mass-spectrometry Dataset Collection" } ], - "label": "Chromatagrams Dataset Collection", + "label": "Mass-spectrometry Dataset Collection", "name": "Input dataset collection", "outputs": [], "position": { diff --git a/workflows/metabomics-lcms-preprocessing/README.md b/workflows/metabomics-lcms-preprocessing/README.md new file mode 100644 index 000000000..d88861808 --- /dev/null +++ b/workflows/metabomics-lcms-preprocessing/README.md @@ -0,0 +1,38 @@ +# Mass spectrometry: LC-MS preprocessing with XCMS + +This workflow is composed with the XCMS tool R package [(Smith, C.A. 2006)](https://bioconductor.org/packages/release/bioc/html/xcms.html) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package [(Kuhl, C 2012)](https://bioconductor.org/packages/release/bioc/html/CAMERA.html). + +🎓 For more information, it is explained in the [Galaxy Training Network tutorial: Mass spectrometry: LC-MS preprocessing with XCMS](https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html) + +## Inputs +### sampleMetadata +The sampleMetadata tabular file corresponds to a table containing information about your samples + +A sample metadata file contains various information for each of your raw files: +- Classes which will be used during the preprocessing steps +- Analytical batches which will be useful for a batch correction step, along with sample types (pool/sample) and injection order +- Different experimental conditions which can be used for statistics +- Any information about samples that you want to keep, in a column format + +The content of your sample metadata file has to be filled by you, since it is not contained in your raw data. Note that you can either: +- Upload an existing metadata file +- Use a template to create one (because it can be painful to get the sample list without misspelling or omission) + - Generate a template with the xcms get a sampleMetadata file tool tool + - Fill it using your favorite table editor (Excel, LibreOffice) + - Upload it within Galaxy + +**Formats:** tab-separated values as tsv, tab, txt, ... + +### Chromatograms Dataset Collection +Mass-spectrometry data files gathered in a Galaxy Dataser Collection + +**Formats:** open format as mzXML, mzMl, mzData and netCDF + +## Main steps +1. MSnbase readMSData: read the mzXML and prepare for xcms +2. XCMS findChromPeaks: peak picking +3. XCMS groupChromPeaks: determining shared ions across samples +4. XCMS adjustRtime: retention time correction +5. XCMS fillChromPeaks: integrating areas of missing peaks +6. CAMERA.annotate: annotation + From 3f28773b65b406c5059e77f525ad2cb1387ce770 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Wed, 22 Nov 2023 10:19:00 +0100 Subject: [PATCH 05/15] Add metabomics-lcms-preprocessing WF - change name, annotation, workflow outputs --- .../CHANGELOG.md | 2 +- ...y__LC-MS_preprocessing_with_XCMS-test.yml} | 2 +- ...rometry__LC-MS_preprocessing_with_XCMS.ga} | 86 +++++++++++++++---- 3 files changed, 73 insertions(+), 17 deletions(-) rename workflows/metabomics-lcms-preprocessing/{LC-MS_preprocessing-test.yml => Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml} (97%) rename workflows/metabomics-lcms-preprocessing/{LC-MS_preprocessing.ga => Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga} (89%) diff --git a/workflows/metabomics-lcms-preprocessing/CHANGELOG.md b/workflows/metabomics-lcms-preprocessing/CHANGELOG.md index 90622474c..6598368b9 100644 --- a/workflows/metabomics-lcms-preprocessing/CHANGELOG.md +++ b/workflows/metabomics-lcms-preprocessing/CHANGELOG.md @@ -2,7 +2,7 @@ All notable changes to this project will be documented in this file. -## [0.1] - 2023-11-22 +## [1.0] - 2023-11-22 First release diff --git a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing-test.yml b/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml similarity index 97% rename from workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing-test.yml rename to workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml index bdcb300f3..bbd3b2a2c 100644 --- a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing-test.yml +++ b/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml @@ -1,4 +1,4 @@ -- doc: Test outline for LC-MS_preprocessing +- doc: Test outline for Mass_spectrometry__LC-MS_preprocessing_with_XCMS job: SampleMetadata: class: File diff --git a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga b/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga similarity index 89% rename from workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga rename to workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga index 1dfe261b5..6d0e77f83 100644 --- a/workflows/metabomics-lcms-preprocessing/LC-MS_preprocessing.ga +++ b/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga @@ -1,18 +1,18 @@ { "a_galaxy_workflow": "true", - "annotation": "Mass spectrometry: LC-MS preprocessing with XCMS\n\nhttps://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html ", + "annotation": "This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).\n\n\nhttps://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html ", "creator": [ { "class": "Organization", "image": "https://raw.githubusercontent.com/workflow4metabolomics/workflow4metabolomics/master/images/logo/logo_w4m-0.1-black-orange.png", "name": "workflow4metabolomics", - "url": "https://workflow4metabolomics.org/" + "url": "https://workflow4metabolomics.org" } ], "format-version": "0.1", "license": "MIT", - "release": "0.1", - "name": "LC-MS preprocessing", + "release": "1.0", + "name": "Mass spectrometry: LC-MS preprocessing with XCMS", "steps": { "0": { "annotation": "", @@ -34,7 +34,7 @@ "top": 151.0066585286458 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "bf49de4d-c959-476c-86e1-6ae621bc915c", @@ -61,7 +61,7 @@ "top": 300.0066585286458 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"mzml\"], \"tag\": null, \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"format\": [\"mzml\", \"mzxml\", \"mzdata\", \"netcdf\"], \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "93611663-3e2a-41d1-a659-52217d5be454", @@ -152,7 +152,18 @@ "type": "tool", "uuid": "b8f69b68-dd61-41c4-9339-d821b14b50dd", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "ticsPdf", + "uuid": "4a8d8533-5b39-49e5-9eeb-b6fb29ecfad4" + }, + { + "label": null, + "output_name": "bpisPdf", + "uuid": "a483b83e-9fc8-4d06-a5d4-a5d49840016d" + } + ] }, "4": { "annotation": "", @@ -274,7 +285,7 @@ ], "position": { "left": 1129, - "top": 176.0066585286458 + "top": 176 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0", @@ -289,7 +300,13 @@ "type": "tool", "uuid": "7d43b889-0799-4ec1-9b0f-1bff1c3a189b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "plotChromPeakDensity", + "uuid": "28f8a44d-db88-4bd8-89b3-bde0bc4948b8" + } + ] }, "7": { "annotation": "", @@ -332,7 +349,13 @@ "type": "tool", "uuid": "656670ac-dfae-41c8-a551-f3ff1f1bb61f", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "rawVSadjustedPdf", + "uuid": "0bf0db72-a5f7-40cc-96a8-c200393d558d" + } + ] }, "8": { "annotation": "", @@ -383,7 +406,13 @@ "type": "tool", "uuid": "fcbec34b-b0d1-4d09-9873-a3c9c95399dc", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "graphs_out", + "uuid": "80858377-f286-48d8-8b8e-edc70f4fbb95" + } + ] }, "9": { "annotation": "", @@ -430,7 +459,18 @@ "type": "tool", "uuid": "95ef16c0-4b3f-44de-99b3-2c4ace994d5f", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "ticsPdf", + "uuid": "72185083-b1c0-4b45-8a91-875873d4fdcb" + }, + { + "label": null, + "output_name": "bpisPdf", + "uuid": "15c97a18-a8af-46da-9c2b-38e9126affa4" + } + ] }, "10": { "annotation": "", @@ -481,7 +521,13 @@ "type": "tool", "uuid": "a6477b12-d89e-48b1-8572-9a86490211a4", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "plotChromPeakDensity", + "uuid": "6547dcea-fd0c-4029-bb47-a71dc6432e70" + } + ] }, "11": { "annotation": "", @@ -533,6 +579,11 @@ "label": "xcms fillChromPeaks dataMatrix", "output_name": "dataMatrix", "uuid": "b716b601-92fa-472c-993b-0769078d2b01" + }, + { + "label": null, + "output_name": "xsetRData", + "uuid": "967392c7-016e-4d7e-8bf6-ce3628113345" } ] }, @@ -582,6 +633,11 @@ "label": "CAMERA.annotate variableMetadata", "output_name": "variableMetadata", "uuid": "9b321589-0f82-4f17-bf9b-faae8c353079" + }, + { + "label": null, + "output_name": "rdata_quick_true", + "uuid": "5fd93902-b994-4124-8646-41b8f2c47b7d" } ] } @@ -594,6 +650,6 @@ "xcms", "GTN" ], - "uuid": "7680429c-e77a-4134-8f4d-90f145e0ca6f", - "version": 2 + "uuid": "4b4dda98-7422-4207-b9bd-62c11ce8e0f0", + "version": 5 } From ad970f27f383945dec4b945bfc840c36bcb5f4ba Mon Sep 17 00:00:00 2001 From: lecorguille Date: Wed, 22 Nov 2023 10:21:02 +0100 Subject: [PATCH 06/15] Add metabomics-lcms-preprocessing WF - fix dockstore.yml --- workflows/metabomics-lcms-preprocessing/.dockstore.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/metabomics-lcms-preprocessing/.dockstore.yml b/workflows/metabomics-lcms-preprocessing/.dockstore.yml index a3ce533f2..56ab96217 100644 --- a/workflows/metabomics-lcms-preprocessing/.dockstore.yml +++ b/workflows/metabomics-lcms-preprocessing/.dockstore.yml @@ -3,8 +3,8 @@ workflows: - name: main subclass: Galaxy publish: true - primaryDescriptorPath: /LC-MS_preprocessing.ga + primaryDescriptorPath: /Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga authors: - name: workflow4metabolomics image: https://raw.githubusercontent.com/workflow4metabolomics/workflow4metabolomics/master/images/logo/logo_w4m-0.1-black-orange.png - url: https://workflow4metabolomics.org/ + url: https://workflow4metabolomics.org From d29ab4f3fb04b099cf0e766cd9a3268f60613e6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Wed, 22 Nov 2023 11:30:38 +0100 Subject: [PATCH 07/15] Update workflows/metabomics-lcms-preprocessing/README.md Co-authored-by: Marius van den Beek --- workflows/metabomics-lcms-preprocessing/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metabomics-lcms-preprocessing/README.md b/workflows/metabomics-lcms-preprocessing/README.md index d88861808..c8bd959eb 100644 --- a/workflows/metabomics-lcms-preprocessing/README.md +++ b/workflows/metabomics-lcms-preprocessing/README.md @@ -1,6 +1,6 @@ # Mass spectrometry: LC-MS preprocessing with XCMS -This workflow is composed with the XCMS tool R package [(Smith, C.A. 2006)](https://bioconductor.org/packages/release/bioc/html/xcms.html) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package [(Kuhl, C 2012)](https://bioconductor.org/packages/release/bioc/html/CAMERA.html). +This workflow uses the XCMS tool R package [(Smith, C.A. 2006)](https://bioconductor.org/packages/release/bioc/html/xcms.html) to extract, filter, align and fill gaps, and uses the CAMERA R package [(Kuhl, C 2012)](https://bioconductor.org/packages/release/bioc/html/CAMERA.html) to annotate isotopes, adducts and fragments. 🎓 For more information, it is explained in the [Galaxy Training Network tutorial: Mass spectrometry: LC-MS preprocessing with XCMS](https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html) From df2462e5bb4ff1b6e7fee7adc97f6de49e59c79a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Wed, 22 Nov 2023 11:30:49 +0100 Subject: [PATCH 08/15] Update workflows/metabomics-lcms-preprocessing/README.md Co-authored-by: Marius van den Beek --- workflows/metabomics-lcms-preprocessing/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metabomics-lcms-preprocessing/README.md b/workflows/metabomics-lcms-preprocessing/README.md index c8bd959eb..b26aa0148 100644 --- a/workflows/metabomics-lcms-preprocessing/README.md +++ b/workflows/metabomics-lcms-preprocessing/README.md @@ -2,7 +2,7 @@ This workflow uses the XCMS tool R package [(Smith, C.A. 2006)](https://bioconductor.org/packages/release/bioc/html/xcms.html) to extract, filter, align and fill gaps, and uses the CAMERA R package [(Kuhl, C 2012)](https://bioconductor.org/packages/release/bioc/html/CAMERA.html) to annotate isotopes, adducts and fragments. -🎓 For more information, it is explained in the [Galaxy Training Network tutorial: Mass spectrometry: LC-MS preprocessing with XCMS](https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html) +🎓 For more information see the [Galaxy Training Network tutorial: Mass spectrometry: LC-MS preprocessing with XCMS](https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html) ## Inputs ### sampleMetadata From e79864821f515f33480900c66244aad47b9b107a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Wed, 22 Nov 2023 11:31:17 +0100 Subject: [PATCH 09/15] Update workflows/metabomics-lcms-preprocessing/README.md Co-authored-by: Marius van den Beek --- workflows/metabomics-lcms-preprocessing/README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/metabomics-lcms-preprocessing/README.md b/workflows/metabomics-lcms-preprocessing/README.md index b26aa0148..39e9a1640 100644 --- a/workflows/metabomics-lcms-preprocessing/README.md +++ b/workflows/metabomics-lcms-preprocessing/README.md @@ -35,4 +35,3 @@ Mass-spectrometry data files gathered in a Galaxy Dataser Collection 4. XCMS adjustRtime: retention time correction 5. XCMS fillChromPeaks: integrating areas of missing peaks 6. CAMERA.annotate: annotation - From 1b6c65ddaef4c81c84d8e65d6c7a2038912ed019 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Wed, 22 Nov 2023 11:31:24 +0100 Subject: [PATCH 10/15] Update workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml Co-authored-by: Marius van den Beek --- .../Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml b/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml index bbd3b2a2c..e9951ff53 100644 --- a/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml +++ b/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml @@ -62,4 +62,3 @@ file: test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv CAMERA.annotate variableMetadata: file: test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv - From d63b7d841aece34ea3c540e30e4713ec359ac2c2 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Wed, 22 Nov 2023 11:43:19 +0100 Subject: [PATCH 11/15] Add metabomics-lcms-preprocessing WF - change path --- .../lcms-preprocessing}/.dockstore.yml | 0 .../lcms-preprocessing}/CHANGELOG.md | 0 .../Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml | 0 .../Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga | 0 .../lcms-preprocessing}/README.md | 0 ...e.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv | 0 ...hromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename workflows/{metabomics-lcms-preprocessing => metabomics/lcms-preprocessing}/.dockstore.yml (100%) rename workflows/{metabomics-lcms-preprocessing => metabomics/lcms-preprocessing}/CHANGELOG.md (100%) rename workflows/{metabomics-lcms-preprocessing => metabomics/lcms-preprocessing}/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml (100%) rename workflows/{metabomics-lcms-preprocessing => metabomics/lcms-preprocessing}/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga (100%) rename workflows/{metabomics-lcms-preprocessing => metabomics/lcms-preprocessing}/README.md (100%) rename workflows/{metabomics-lcms-preprocessing => metabomics/lcms-preprocessing}/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv (100%) rename workflows/{metabomics-lcms-preprocessing => metabomics/lcms-preprocessing}/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv (100%) diff --git a/workflows/metabomics-lcms-preprocessing/.dockstore.yml b/workflows/metabomics/lcms-preprocessing/.dockstore.yml similarity index 100% rename from workflows/metabomics-lcms-preprocessing/.dockstore.yml rename to workflows/metabomics/lcms-preprocessing/.dockstore.yml diff --git a/workflows/metabomics-lcms-preprocessing/CHANGELOG.md b/workflows/metabomics/lcms-preprocessing/CHANGELOG.md similarity index 100% rename from workflows/metabomics-lcms-preprocessing/CHANGELOG.md rename to workflows/metabomics/lcms-preprocessing/CHANGELOG.md diff --git a/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml b/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml similarity index 100% rename from workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml rename to workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml diff --git a/workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga b/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga similarity index 100% rename from workflows/metabomics-lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga rename to workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga diff --git a/workflows/metabomics-lcms-preprocessing/README.md b/workflows/metabomics/lcms-preprocessing/README.md similarity index 100% rename from workflows/metabomics-lcms-preprocessing/README.md rename to workflows/metabomics/lcms-preprocessing/README.md diff --git a/workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv b/workflows/metabomics/lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv similarity index 100% rename from workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv rename to workflows/metabomics/lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv diff --git a/workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv b/workflows/metabomics/lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv similarity index 100% rename from workflows/metabomics-lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv rename to workflows/metabomics/lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv From 26d336ff10d6a92decdd726c676cff13d09a8e6e Mon Sep 17 00:00:00 2001 From: lecorguille Date: Wed, 22 Nov 2023 14:42:26 +0100 Subject: [PATCH 12/15] Add metabomics-lcms-preprocessing WF - fix tests.yml name --- ...=> Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename workflows/metabomics/lcms-preprocessing/{Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml => Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml} (100%) diff --git a/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml b/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml similarity index 100% rename from workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-test.yml rename to workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml From 0db2f5fd9bf5c9105093526e00f50b957596eff4 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Wed, 22 Nov 2023 14:47:11 +0100 Subject: [PATCH 13/15] Add metabomics-lcms-preprocessing WF - fix dockerstore --- workflows/metabomics/lcms-preprocessing/.dockstore.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/workflows/metabomics/lcms-preprocessing/.dockstore.yml b/workflows/metabomics/lcms-preprocessing/.dockstore.yml index 56ab96217..682863271 100644 --- a/workflows/metabomics/lcms-preprocessing/.dockstore.yml +++ b/workflows/metabomics/lcms-preprocessing/.dockstore.yml @@ -4,6 +4,8 @@ workflows: subclass: Galaxy publish: true primaryDescriptorPath: /Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga + testParameterFiles: + - /Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml authors: - name: workflow4metabolomics image: https://raw.githubusercontent.com/workflow4metabolomics/workflow4metabolomics/master/images/logo/logo_w4m-0.1-black-orange.png From ecd5f766ac49133c7dbeb38c9e823c730e1d6805 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Thu, 23 Nov 2023 09:41:09 +0100 Subject: [PATCH 14/15] Update workflows/metabomics/lcms-preprocessing/README.md Co-authored-by: Lucille Delisle --- workflows/metabomics/lcms-preprocessing/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metabomics/lcms-preprocessing/README.md b/workflows/metabomics/lcms-preprocessing/README.md index 39e9a1640..d75cffdf1 100644 --- a/workflows/metabomics/lcms-preprocessing/README.md +++ b/workflows/metabomics/lcms-preprocessing/README.md @@ -17,7 +17,7 @@ A sample metadata file contains various information for each of your raw files: The content of your sample metadata file has to be filled by you, since it is not contained in your raw data. Note that you can either: - Upload an existing metadata file - Use a template to create one (because it can be painful to get the sample list without misspelling or omission) - - Generate a template with the xcms get a sampleMetadata file tool tool + - Generate a template with the `xcms get a sampleMetadata file` tool available in Galaxy - Fill it using your favorite table editor (Excel, LibreOffice) - Upload it within Galaxy From b39846e0113a92960140d23b5b822c8f51165e87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Thu, 23 Nov 2023 09:41:37 +0100 Subject: [PATCH 15/15] Update README.md --- workflows/metabomics/lcms-preprocessing/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metabomics/lcms-preprocessing/README.md b/workflows/metabomics/lcms-preprocessing/README.md index d75cffdf1..390aa0aa3 100644 --- a/workflows/metabomics/lcms-preprocessing/README.md +++ b/workflows/metabomics/lcms-preprocessing/README.md @@ -23,7 +23,7 @@ The content of your sample metadata file has to be filled by you, since it is no **Formats:** tab-separated values as tsv, tab, txt, ... -### Chromatograms Dataset Collection +### Mass-spectrometry Dataset Collection Mass-spectrometry data files gathered in a Galaxy Dataser Collection **Formats:** open format as mzXML, mzMl, mzData and netCDF