name: "hamronization_rgi"
description: Tool to convert and summarize RGI outputs using the hAMRonization specification.
keywords:
  - amr
  - antimicrobial resistance
  - arg
  - antimicrobial resistance genes
  - reporting
  - rgi
tools:
  - hamronization:
      description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
      homepage: "https://github.com/pha4ge/hAMRonization/"
      documentation: "https://github.com/pha4ge/hAMRonization/"
      tool_dev_url: "https://github.com/pha4ge/hAMRonization"
      doi: ""
      licence: "['GNU Lesser General Public v3 (LGPL v3)']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - report:
      type: file
      description: Output .txt file from RGI
      pattern: "*.txt"
  - format:
      type: value
      description: Type of report file to be produced
      pattern: "tsv|json"
  - software_version:
      type: value
      description: Version of DeepARG used
      pattern: "[0-9].[0-9].[0-9]"
  - reference_db_version:
      type: value
      description: Database version of DeepARG used
      pattern: "[0-9].[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"
  - json:
      type: file
      description: hAMRonised report in JSON format
      pattern: "*.json"
  - tsv:
      type: file
      description: hAMRonised report in TSV format
      pattern: "*.json"

authors:
  - "@louperelo"