name: windowmasker_mkcounts
description: A program to generate frequency counts of repetitive units.
keywords:
  - fasta
  - interval
  - windowmasker
tools:
  - windowmasker:
      description: |
        A program to mask highly repetitive and low complexity DNA sequences within a genome.
      homepage: https://github.com/ncbi/ncbi-cxx-toolkit-public
      documentation: https://ncbi.github.io/cxx-toolkit/
      licence: ["MIT"]
      identifier: biotools:windowmasker
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - ref:
        type: file
        description: An input nucleotide fasta file.
output:
  - counts:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.txt":
          type: file
          description: A file containing frequency counts of repetitive units.
          pattern: "*.txt"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@DLBPointon"
maintainers:
  - "@DLBPointon"
