Merge pull request #606 from PratikDJagtap/main

Adding Clinical Metaproteomics-Verification

workflows/proteomics/clinicalmp/clinicalmp-verification/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /clinicalmp-verification.ga
+  testParameterFiles:
+  - /clinicalmp-verification-tests.yml
+  authors:
+  - name: Pratik Jagtap
+    orcid: 0000-0003-0984-0973

workflows/proteomics/clinicalmp/clinicalmp-verification/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2024-11-19
+First release.

workflows/proteomics/clinicalmp/clinicalmp-verification/README.md

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+# Clinical Metaproteomics 3: Verification
+This workflow uses the PepQuery tool to verify peptides discovered with the clinical metaproteomics discovery workflow.
+The PepQuery tool outputs verified peptides that can be used to generate a verified protein database that can be used for the clinical metaproteomics quantitation workflow.
+
+More background on this workflow can be found in the [Clinical Metaproteomics 3: Verification tutorial](https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html)
+
+## Inputs datasets
+
+### Tabular Input Files
+- SGPS peptide report
+- MaxQuant Peptide report
+- Distinct Peptides for PepQuery
+
+### Search Databases (FASTA)
+- Uniprot HUMAN database
+- cRAP
+
+### MSMS files
+The tandem MS/MS files can be downloaded via Zenodo. These MS/MS input files are pilot datasets from Papanicolaou test samples from healthy, benign and ovarian cancer patients. 
+
+## Input Values
+For PepQuery:
+- Search Tolerances
+- Digestion Enzyme
+- Peptide Length
+- Modifications
+
+## Processing
+Extract protein sequences for the verified peptides.

workflows/proteomics/clinicalmp/clinicalmp-verification/clinicalmp-verification-tests.yml

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+- doc: Test outline for Clinical Metaproteomics Verification Workflow
+  job:
+    SGPS peptide report:
+      class: File
+      path: test-data/SGPS_peptide-report.tabular
+      filetype: tabular
+    Distinct Peptides for PepQuery:
+      class: File
+      path: test-data/Distinct_Peptides_for_PepQuery.tabular
+      filetype: tabular
+    MaxQuant peptide report:
+      class: File
+      path: test-data/MaxQuant-peptide-report.tabular
+      filetype: tabular
+    Tandem Mass Spectrometry (MS/MS) datasets:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.mgf
+        location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.mgf
+      - class: File
+        identifier: PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.mgf
+        location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.mgf
+      - class: File
+        identifier: PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.mgf
+        location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.mgf
+      - class: File
+        identifier: PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.mgf
+        location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.mgf
+  outputs:
+    Human UniProt+Isoforms FASTA:
+      asserts:
+        has_text: 
+          text: ">sp"
+    cRAP:
+      path: test-data/cRAP.fasta
+    Human UniProt+Isoforms+cRAP FASTA:
+      asserts:
+        has_text: 
+          text: ">sp"
+    Peptide and Protein from Peptide Reports:
+      path: test-data/Peptide_and_Protein_from_Peptide_Reports.tabular
+    Uniprot ID from verified Peptides:
+      path: test-data/Uniprot-ID_from_verified_Peptides.tabular
+    Quantitation Database for MaxQuant:
+      asserts:
+        has_text: 
+          text: ">tr"