name: rgi_main
description: Predict antibiotic resistance from protein or nucleotide data
keywords:
  - bacteria
  - fasta
  - antibiotic resistance
tools:
  - rgi:
      description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website
      homepage: https://card.mcmaster.ca
      documentation: https://github.com/arpcard/rgi
      tool_dev_url: https://github.com/arpcard/rgi
      doi: "10.1093/nar/gkz935"
      licence: ["https://card.mcmaster.ca/about"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Nucleotide or protein sequences in FASTA format
      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"

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"
  - json:
      type: file
      description: JSON formatted file with RGI results
      pattern: "*.{json}"
  - tsv:
      type: file
      description: Tab-delimited file with RGI results
      pattern: "*.{txt}"
  - tool_version:
      type: string
      description: The version of the tool in string format (useful for downstream tools such as hAMRronization)
  - db_version:
      type: string
      description: The version of the used database in string format (useful for downstream tools such as hAMRronization)
authors:
  - "@rpetit3"
  - "@jfy133"