name: proteomicslfq
description: ProteomicsLFQ performs label-free quantification of peptides and proteins.
keywords:
  - label-free
  - OpenMS
  - quantification
tools:
  - ProteomicsLFQ:
      description: |
        ProteomicsLFQ performs label-free quantification of peptides and proteins.
      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_ProteomicsLFQ.html
      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_ProteomicsLFQ.html
input:
  - mzmls:
      type: file
      description: Input Spectra in mzML format
      pattern: "*.mzML"
  - id_files:
      type: file
      description: Identifications in idXML or mzIdentML format with posterior error probabilities as score type.
      pattern: "*.idXML"
  - expdes:
      type: file
      description: An experimental design file
      pattern: "*.tsv"
  - fasta:
      type: file
      description: A protein database in with appended decoy sequences in FASTA format.
      pattern: "*.{fasta,fa}"
output:
  - out_mztab:
      type: file
      description: mzTab file with analysis results
      pattern: "*.mzTab"
  - out_consensusXML:
      type: file
      description: ConsensusXML file for visualization and further processing in OpenMS.
      pattern: "*.consensusXML"
  - out_msstats:
      type: file
      description: MSstats file with analysis results for statistical downstream analysis in MSstats.
      pattern: "*msstats_in.csv"
  - out_triqler:
      type: file
      description: Triqler file with analysis results for statistical downstream analysis in Triqler.
      pattern: "*triqler_in.csv"
  - log:
      type: file
      description: log file
      pattern: "*.log"
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
authors:
  - "@daichengxin"
