name: diannsummary
description: A module for summarization of results from DIA-NN analysis.
keywords:
  - DIA-NN
  - DIA
tools:
  - DIA-NN:
      description: |
        DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing by Demichev.
      homepage: https://github.com/vdemichev/DiaNN
      documentation: https://github.com/vdemichev/DiaNN
input:
  - empirical_library:
      type: file
      description: Empirical spectral library generated by DIA-NN
      pattern: "*.tsv"
  - mzMLs:
      type: file
      description: Spectra files in mzML format.
      pattern: "*.mzML"
  - fasta:
      type: file
      description: Protein sequence database in Fasta format.
      pattern: "*.{fasta,fa}"
  - quant:
      type: file
      description: Identification and Quantification file from DIA-NN.
      pattern: "*.quant"
output:
  - main_report:
      type: file
      description: A text table containing precursor and protein IDs, as well as plenty of associated information.
      pattern: "*.tsv"
  - pr_matrix:
      type: file
      description: A text table containing normalized quantities for precursors. They are filtered at 1% FDR, using both global and run-specific q-values for precursors
      pattern: "*.tsv"
  - pg_matrix:
      type: file
      description: A text table containing normalized quantities for protein groups. They are filtered at 1% FDR, using global q-values for protein groups
      pattern: "*.tsv"
  - gg_matrix:
      type: file
      description: A text table containing normalized quantities for gene groups.
      pattern: "*.tsv"
  - log:
      type: file
      description: DIA-NN log file
      pattern: "diannsummary.log"
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
authors:
  - "@daichengxin"
