name: krona_ktimporttaxonomy
description: KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.
keywords:
  - plot
  - taxonomy
  - interactive
  - html
  - visualisation
  - krona chart
tools:
  - krona:
      description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
      homepage: https://github.com/marbl/Krona/wiki/KronaTools
      documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
      tool_dev_url:
      doi: https://doi.org/10.1186/1471-2105-12-385
      licence:

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - database:
      type: file
      description: |
        Path to the taxonomy database .tab file downloaded by krona/ktUpdateTaxonomy
        The file will be saved under a folder named "taxonomy" as "taxonomy/taxonomy.tab".
        The parent folder will be passed as argument to ktImportTaxonomy.
  - report:
      type: file
      description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores.  Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3.  Lines beginning with # will be ignored."
      pattern: "*.{tsv}"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - html:
      type: file
      description: A html file containing an interactive krona plot.
      pattern: "*.{html}"

authors:
  - "@mjakobs"