name: prodigal
description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a
  microbial (bacterial and archaeal) gene finding program
keywords:
  - prokaryotes
  - gene finding
  - microbial
tools:
  - prodigal:
      description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
        is a microbial (bacterial and archaeal) gene finding program
      homepage: https://github.com/hyattpd/Prodigal
      documentation: https://github.com/hyattpd/prodigal/wiki
      tool_dev_url: https://github.com/hyattpd/Prodigal
      doi: "10.1186/1471-2105-11-119"
      licence: ["GPL v3"]
      identifier: biotools:prodigal
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - genome:
        type: file
        description: fasta/fasta.gz file
        ontologies: []
  - output_format:
      type: string
      description: Output format ("gbk"/"gff"/"sqn"/"sco")
output:
  gene_annotations:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}.${output_format}.gz:
          type: file
          description: gene annotations in output_format given as input
          pattern: "*.{output_format}"
          ontologies: []
  nucleotide_fasta:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}.fna.gz:
          type: file
          description: nucleotide sequences file
          pattern: "*.{fna}"
          ontologies: []
  amino_acid_fasta:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}.faa.gz:
          type: file
          description: protein translations file
          pattern: "*.{faa}"
          ontologies: []
  all_gene_annotations:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}_all.txt.gz:
          type: file
          description: complete starts file
          pattern: "*.{_all.txt}"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@grst"
maintainers:
  - "@grst"
