name: "plasmidfinder"
description: Identify plasmids in bacterial sequences and assemblies
keywords:
  - fasta
  - fastq
  - plasmid
tools:
  - "plasmidfinder":
      description: "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria."
      homepage: "https://cge.cbs.dtu.dk/services/PlasmidFinder/"
      documentation: "https://bitbucket.org/genomicepidemiology/plasmidfinder"
      tool_dev_url: "https://bitbucket.org/genomicepidemiology/plasmidfinder"
      doi: "10.1128/AAC.02412-14"
      licence: "['Apache-2.0']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - seqs:
      type: file
      description: Input FASTA or FASTQ formatted genome sequences
      pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}"

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"
  - json:
      type: file
      description: The results from analysis in JSON format
      pattern: "*.json"
  - txt:
      type: file
      description: The summary of results from analysis
      pattern: "*.txt"
  - tsv:
      type: file
      description: The results from analysis in TSV format
      pattern: "*.tsv"
  - genome_seq:
      type: file
      description: FASTA of sequences in the input with a hit
      pattern: "*-hit_in_genome_seq.fsa"
  - plasmid_seq:
      type: file
      description: FASTA of plasmid sequences with a hit against the input
      pattern: "*-plasmid_seqs.fsa"
authors:
  - "@rpetit3"