name: plasmidid
description: assembles bacterial plasmids
keywords:
  - assembly
  - plasmid
  - bacterial
tools:
  - plasmidid:
      description: Pipeline for plasmid identification and reconstruction
      homepage: https://github.com/BU-ISCIII/plasmidID/wiki
      documentation: https://github.com/BU-ISCIII/plasmidID#readme
      tool_dev_url: https://github.com/BU-ISCIII/plasmidID
      doi: ""
      licence: ['GPL v3']

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
  - 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 ]
  - html:
      type: file
      description: html file with results rendered
      pattern: "*.{html}"
  - tab:
      type: file
      description: Results in a tabular file
      pattern: "*.{tab}"
  - images:
      type: directory
      description: Directory containing the images produced by plasmidid
      pattern: "images"
  - logs:
      type: directory
      description: Directory containing the logs produced by plasmidid
      pattern: "logs"
  - data:
      type: directory
      description: Directory containing the data produced by plasmidid
      pattern: "data"
  - database:
      type: directory
      description: Directory containing the database produced by plasmidid
      pattern: "database"
  - fasta_files:
      type: directory
      description: Directory containing the fasta files produced by plasmidid
      pattern: "fasta_files"
  - kmer:
      type: directory
      description: Directory containing the kmer files produced by plasmidid
      pattern: "database"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"

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