Merge pull request galaxyproject#292 from workflow4metabolomics/w4m_lcms

Add metabomics-lcms-preprocessing WF
lldelisle · Nov 23, 2023 · cc6f30f · cc6f30f
2 parents ea509c0 + b39846e
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diff --git a/workflows/metabomics/lcms-preprocessing/.dockstore.yml b/workflows/metabomics/lcms-preprocessing/.dockstore.yml
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+version: 1.2
+workflows:
+- name: main
+  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
+    url: https://workflow4metabolomics.org
diff --git a/workflows/metabomics/lcms-preprocessing/CHANGELOG.md b/workflows/metabomics/lcms-preprocessing/CHANGELOG.md
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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [1.0] - 2023-11-22
+
+First release
+
diff --git a/.../metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml b/.../metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS-tests.yml
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+- doc: Test outline for Mass_spectrometry__LC-MS_preprocessing_with_XCMS
+  job:
+    SampleMetadata:
+      class: File
+      identifier: sampleMetadata.tsv
+      location: https://zenodo.org/records/10130758/files/sampleMetadata_12samp_completed.tsv
+      filetype: tabular
+    Mass-spectrometry Dataset Collection:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: Blanc05.mzML
+        location: https://zenodo.org/record/10130758/files/Blanc05.mzML
+        filetype: mzml
+      - class: File
+        identifier: Blanc10.mzML
+        location: https://zenodo.org/record/10130758/files/Blanc10.mzML
+        filetype: mzml
+      - class: File
+        identifier: Blanc16.mzML
+        location: https://zenodo.org/record/10130758/files/Blanc16.mzML
+        filetype: 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