clinicalmp-verification-tests.yml

- 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"