name: "ampir"
description: A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.
keywords:
  - ampir
  - amp
  - antimicrobial peptide prediction
tools:
  - "ampir":
      description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale."
      homepage: "https://github.com/Legana/ampir"
      documentation: "https://cran.r-project.org/web/packages/ampir/index.html"
      tool_dev_url: "https://github.com/Legana/ampir"
      doi: "10.1093/bioinformatics/btaa653"
      licence: ["GPL v2"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - faa:
      type: file
      description: FASTA file containing amino acid sequences
      pattern: "*.{faa,fasta}"
  - model:
      type: string
      description: Built-in model for AMP prediction
      pattern: "{precursor,mature}"
  - min_length:
      type: integer
      description: Minimum protein length for which predictions will be generated
      pattern: "[0-9]+"
  - min_probability:
      type: number
      description: Cut-off for AMP prediction
      pattern: "[0-9].[0-9]+"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - amps_faa:
      type: file
      description: File containing AMP predictions in amino acid FASTA format
      pattern: "*.{faa}"
  - amps_tsv:
      type: file
      description: File containing AMP predictions in TSV format
      pattern: "*.tsv"

authors:
  - "@jasmezz"
