name: abacas
description: contiguate draft genome assembly
keywords:
  - genome
  - assembly
  - contiguate
tools:
  - abacas:
      description: |
        ABACAS is intended to rapidly contiguate (align, order, orientate),
        visualize and design primers to close gaps on shotgun assembled
        contigs based on a reference sequence.
      homepage: http://abacas.sourceforge.net/documentation.html
      documentation: http://abacas.sourceforge.net/documentation.html
      tool_dev_url: None
      doi: "10.1093/bioinformatics/btp347"
      licence: ["GPL v2-or-later"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - scaffold:
      type: file
      description: Fasta file containing scaffold
      pattern: "*.{fasta,fa}"
  - fasta:
      type: file
      description: FASTA reference file
      pattern: "*.{fasta,fa}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - results:
      type: files
      description: |
        List containing abacas output files
        [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
        'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
        'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
        'test.abacas.tab', 'test.abacas.unused.contigs.out',
        'test.abacas.MULTIFASTA.fa' ]
      pattern: "*.{abacas}*"

  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@joseespinosa"
  - "@drpatelh"
