name: agat_sq_stat_basic
namespace: agat
description: |
  The script aims to provide basic statistics of a gtf/gff file.
keywords: [gene annotations, gff, statistics]
links:
  homepage: https://github.com/NBISweden/AGAT
  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sq_stat_basic.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
requirements:
 - commands: [agat]
authors:
  - __merge__: /src/_authors/leila_paquay.yaml
    roles: [ author, maintainer ]
argument_groups:
  - name: Inputs
    arguments:
      - name: --gff
        alternatives: [-i, --file, --input]
        description: |
          Input GTF/GFF file.
        type: file
        required: true
        multiple: true
        direction: input
        example: input.gff
      - name: --genome_size
        alternatives: [-g]
        description: |
          That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide an INTEGER. Or you can also pass a fasta file using the argument --genome_size_fasta. If both are provided, only the value of --genome_size will be considered.
        type: integer
        required: false
        direction: input
        example: 10000
      - name: --genome_size_fasta
        description: |
          That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide the genome in fasta format. Or you can also pass the size directly as an integer using the argument --genome_size. If you provide the fasta, the genome size will be calculated on the fly. If both are provided, only the value of --genome_size will be considered.
        type: file
        required: false
        direction: input
        example: genome.fasta
  - name: Outputs
    arguments:
      - name: --output
        alternatives: [-o]
        description: |
          Output file. The result is in tabulate format.
        type: file
        direction: output
        required: true
        example: output.txt
  - name: Arguments
    arguments:
      - name: --inflate
        description: |
            Inflate the statistics taking into account feature with
            multi-parents. Indeed to avoid redundant information, some gff
            factorize identical features. e.g: one exon used in two
            different isoform will be defined only once, and will have
            multiple parent. By default the script count such feature only
            once. Using the inflate option allows to count the feature and
            its size as many time there are parents.
        type: boolean_true
      - name: --config
        alternatives: [-c]
        description: |
          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. 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