name: "gamma"
description: Gene Allele Mutation Microbial Assessment
keywords:
  - gamma
  - gene-calling
tools:
  - "gamma":
      description: "Tool for Gene Allele Mutation Microbial Assessment"
      homepage: "https://github.com/rastanton/GAMMA"
      documentation: "https://github.com/rastanton/GAMMA"
      tool_dev_url: "https://github.com/rastanton/GAMMA"
      doi: "10.1093/bioinformatics/btab607"
      licence: "['Apache License 2.0']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: FASTA file
      pattern: "*.{fa,fasta}"
  - db:
      type: file
      description: Database in FASTA format
      pattern: "*.{fa,fasta}"

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"

  - gamma:
      type: file
      description: GAMMA file with annotated gene matches
      pattern: "*.{gamma}"

  - psl:
      type: file
      description: PSL file with all gene matches found
      pattern: "*.{psl}"

  - gff:
      type: file
      description: GFF file
      pattern: "*.{gff}"

  - fasta:
      type: file
      description: multifasta file of the gene matches
      pattern: "*.{fasta}"

authors:
  - "@sateeshperi"
  - "@rastanton"
