name: proteinquantifier
description: Compute peptide and protein abundances from annotated feature/consensus maps or from identification results.
keywords:
  - abundances
  - OpenMS
tools:
  - ProteinQuantifier:
      description: |
        Compute peptide and protein abundances from annotated feature/consensus maps or from identification results.
      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinQuantifier.html
      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinQuantifier.html
input:
  - epi_filt_resolve:
      type: file
      description: |
        Input file (data annotated with identifications)
      pattern: "*.{featureXML,consensusXML,idXML}"
output:
  - protein_out:
      type: file
      description: Output file for protein abundances
      pattern: "*protein_openms.csv"
  - peptide_out:
      type: file
      description: Output file for peptide abundances
      pattern: "*peptide_openms.csv"
  - out_mztab:
      type: file
      description: Output file (mzTab)
      pattern: "*.mzTab"
  - log:
      type: file
      description: log file
      pattern: "*.log"
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
authors:
  - "@daichengxin"
