name: hamronization_summarize
description: Tool to summarize and combine all hAMRonization reports into a single file
keywords:
  - amr
  - antimicrobial resistance
  - reporting
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

      licence: ["GNU Lesser General Public v3 (LGPL v3)"]

input:
  - reports:
      type: file
      description: List of multiple hAMRonization reports in either JSON or TSV format
      pattern: "*.{json,tsv}"
  - format:
      type: value
      description: Type of final combined report file to be produced
      pattern: "tsv|json|interactive"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - json:
      type: file
      description: hAMRonised summary in JSON format
      pattern: "*.json"
  - tsv:
      type: file
      description: hAMRonised summary in TSV format
      pattern: "*.json"
  - html:
      type: file
      description: hAMRonised summary in HTML format
      pattern: "*.html"

authors:
  - "@jfy133"
