name: "agat_spkeeplongestisoform"
description: Filters GFF records to keep only the longest isoform per gene
keywords:
  - gff
  - gtf
  - filter
  - isoform
  - gene
  - longest
  - agat
tools:
  - "agat":
      description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene
        annotations in any GTF/GFF format."
      homepage: "https://agat.readthedocs.io/en/latest/"
      documentation: "https://agat.readthedocs.io/en/latest/"
      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:'sample1', single_end:false ]`
    - gxf:
        type: file
        description: Annotation file in GFF/GTF format
        pattern: "*.{gff, gtf}"
        ontologies: []
  - config:
      type: file
      description: |
        Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,
        otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml
        locally type: "agat config --expose". The --config option gives you the possibility to use your
        own AGAT config file (located elsewhere or named differently).
      pattern: "*.yaml"
      ontologies:
        - edam: http://edamontology.org/format_3750 # YAML
output:
  gff:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
          pattern: "*.gff"
      - ${output}:
          type: file
          description: Output GFF3 file
          pattern: "*.longest.gff"
          ontologies: []
  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:
  - "@Juke34"
maintainers:
  - "@Juke34"
