name: agat_spstatistics
description: |
  Provides different type of statistics in text format from a GFF/GTF annotation file
keywords:
  - genome
  - gff
  - gtf
  - statistics
tools:
  - agat:
      description: "AGAT is a toolkit for manipulation and getting information from
        GFF/GTF files"
      homepage: "https://github.com/NBISweden/AGAT"
      documentation: "https://agat.readthedocs.io/"
      tool_dev_url: "https://github.com/NBISweden/AGAT"
      doi: "10.5281/zenodo.3552717"
      licence: ["GPL v3"]
      identifier: biotools:AGAT
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - gff:
        type: file
        description: Annotation file in GFF3/GTF format
        pattern: "*.{gff, gtf}"
        ontologies:
          - edam: "http://edamontology.org/format_1975" # GFF3
          - edam: "http://edamontology.org/format_2306" # GTF
output:
  stats_txt:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - "*.txt":
          type: file
          description: Output of Statistics execution
          pattern: "*.{txt}"
          ontologies:
            - edam: "http://edamontology.org/format_2330" # Plain text
  versions_agat:
    - - ${task.process}:
          type: string
          description: The name of the process
      - agat:
          type: string
          description: The name of the tool
      - agat --version | sed 's/v//':
          type: eval
          description: The expression to obtain the version of the tool
topics:
  versions:
    - - ${task.process}:
          type: string
          description: The name of the process
      - agat:
          type: string
          description: The name of the tool
      - agat --version | sed 's/v//':
          type: eval
          description: The expression to obtain the version of the tool
authors:
  - "@toniher"
maintainers:
  - "@toniher"
  - "@gallvp"
