Update for version 0.1

.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

.github/workflows/wftest.yml

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+name: Periodic workflow test
+on:
+  schedule:
+    - cron: '0 3 * * *'
+  workflow_dispatch:
+jobs:
+  setup:
+    name: Setup cache
+    uses: galaxyproject/iwc/.github/workflows/setup.yml@main
+    with:
+      galaxy-fork: galaxyproject
+  test:
+    name: Test workflow
+    needs: setup
+    uses: galaxyproject/iwc/.github/workflows/test_workflows.yml@main
+    with:
+      galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }}
+      galaxy-fork: galaxyproject
+      repository-list: '.'
+      check-outputs: true

CHANGELOG.md

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

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.

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"