name: agat_convert_bed2gff
namespace: agat
description: |
  The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).
keywords: [gene annotations, GFF conversion]
links:
  homepage: https://github.com/NBISweden/AGAT
  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html
  issue_tracker: https://github.com/NBISweden/AGAT/issues
  repository: https://github.com/NBISweden/AGAT
references: 
  doi: 10.5281/zenodo.3552717
license: GPL-3.0
authors:
  - __merge__: /src/_authors/leila_paquay.yaml
    roles: [ author, maintainer ]
argument_groups:
  - name: Inputs
    arguments:
      - name: --bed
        description: Input bed file that will be converted.
        type: file
        required: true
        direction: input
        example: input.bed
  - name: Outputs
    arguments:       
      - name: --output
        alternatives: [-o, --out, --outfile, --gff]
        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
        type: file
        direction: output
        required: true
        example: output.gff
  - name: Arguments
    arguments:
      - name: --source
        description: |
          The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
        type: string
        required: false
        example: Stringtie
      - name: --primary_tag
        description: |
          The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
        type: string
        required: false
        example: gene
      - name: --inflate_off
        description: |
          By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.
        type: boolean_true
      - name: --inflate_type
        description: |
          Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
        type: string
        required: false
        example: exon
      - name: --verbose
        description: add verbosity
        type: boolean_true
      - name: --config
        alternatives: [-c]
        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 orignal 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).
        type: file
        required: false
        example: custom_agat_config.yaml
resources:
  - type: bash_script
    path: script.sh
test_resources:
  - type: bash_script
    path: test.sh
  - type: file
    path: test_data
engines:
  - type: docker
    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
    setup:
      - type: docker
        run: |
          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
runners:
  - type: executable
  - type: nextflow