name: gffread
description: Validate, filter, convert and perform various other operations on GFF
  files
keywords:
  - gff
  - conversion
  - validation
tools:
  - gffread:
      description: GFF/GTF utility providing format conversions, region filtering, FASTA
        sequence extraction and more.
      homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
      documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
      tool_dev_url: https://github.com/gpertea/gffread
      doi: 10.12688/f1000research.23297.1
      licence: ["MIT"]
      identifier: biotools:gffread
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing meta data
          e.g. [ id:'test' ]
    - gff:
        type: file
        description: A reference file in either the GFF3, GFF2 or GTF format.
        pattern: "*.{gff, gtf}"
        ontologies: []
  - fasta:
      type: file
      description: A multi-fasta file with the genomic sequences
      pattern: "*.{fasta,fa,faa,fas,fsa}"
      ontologies: []
output:
  gtf:
    - - meta:
          type: map
          description: |
            Groovy Map containing meta data
            e.g. [ id:'test' ]
      - "*.gtf":
          type: file
          description: GTF file resulting from the conversion of the GFF input file
            if '-T' argument is present
          pattern: "*.{gtf}"
          ontologies: []
  gffread_gff:
    - - meta:
          type: map
          description: |
            Groovy Map containing meta data
            e.g. [ id:'test' ]
      - "*.gff3":
          type: file
          description: GFF3 file resulting from the conversion of the GFF input file
            if '-T' argument is absent
          pattern: "*.gff3"
          ontologies: []
  gffread_fasta:
    - - meta:
          type: map
          description: |
            Groovy Map containing meta data
            e.g. [ id:'test' ]
      - "*.fasta":
          type: file
          description: Fasta file produced when either of '-w', '-x', '-y' parameters
            is present
          pattern: "*.fasta"
          ontologies: []
  versions_gffread:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - gffread:
          type: string
          description: The tool name
      - gffread --version 2>&1:
          type: eval
          description: The expression to obtain the version of the tool

topics:
  versions:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - gffread:
          type: string
          description: The tool name
      - gffread --version 2>&1:
          type: eval
          description: The expression to obtain the version of the tool

authors:
  - "@edmundmiller"
maintainers:
  - "@edmundmiller"
  - "@gallvp"
