name: ismapper
description: Identify insertion sites positions in bacterial genomes
keywords:
  - fastq
  - insertion sequences
tools:
  - ismapper:
      description: A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes.
      homepage: https://github.com/jhawkey/IS_mapper
      documentation: https://github.com/jhawkey/IS_mapper
      tool_dev_url: https://github.com/jhawkey/IS_mapper
      doi: "https://doi.org/10.1186/s12864-015-1860-2"
      licence: ["BSD-3-Clause"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: A set of paired-end FASTQ files
      pattern: "*.{fastq.gz,fq.gz}"
  - reference:
      type: file
      description: Reference genome in GenBank format
      pattern: "*.{gbk}"
  - query:
      type: file
      description: Insertion sequences to query in FASTA format
      pattern: "*.{fasta,fa}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - results:
      type: directory
      description: Directory containing ISMapper result files
      pattern: "*/*"

authors:
  - "@rpetit3"