name: hamronization_deeparg description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification keywords: - amr - antimicrobial resistance - reporting - deeparg tools: - hamronization: description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md 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 .mapping.ARG file from DeepARG pattern: "*.mapping.ARG" - 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]" 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: - "@jfy133"