name: maxquant_lfq
description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
keywords:
  - sort
tools:
  - maxquant:
      description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
      homepage: None
      documentation: None
      tool_dev_url: None
      doi: ""
      licence: ['http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - raw: 
      type: file 
      description: raw files with mass spectra
      pattern: "*.{raw,RAW,Raw}"

  - fasta:
      type: file 
      description: fasta file with protein sequences
      pattern: "*.{fasta}"

  - parfile:
      type: file 
      description: MaxQuant parameter file (XML)
      pattern: "*.{xml}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - maxquant_txt:
      type: file
      description: tables with peptides and protein information
      pattern: "*.{txt}"

authors:
  - "@veitveit"