# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "taxonkit_lineage"
description: Convert taxonids to taxon lineages
keywords:
  - taxonomy
  - taxids
  - taxon name
  - conversion
tools:
  - "taxonkit":
      description: "A Cross-platform and Efficient NCBI Taxonomy Toolkit"
      homepage: "https://bioinf.shenwei.me/taxonkit/"
      documentation: "https://bioinf.shenwei.me/taxonkit/usage/#name2taxid"
      tool_dev_url: "https://github.com/shenwei356/taxonkit"
      doi: "10.1016/j.jgg.2021.03.006"
      licence: ["MIT"]
      identifier: biotools:taxonkit

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - taxid:
        type: string
        description: Taxon id to look up (provide either this or taxidfile, not both)
    - taxidfile:
        type: file
        description: File with taxon ids to look up, each on their own line (provide
          either this or name, not both; the file can contain other information, see
          the tool's docs)
        ontologies: []
  - taxdb:
      type: file
      description: Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
      ontologies: []
output:
  tsv:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*.tsv":
          type: file
          description: TSV file with added taxon lineages
          pattern: "*.tsv"
          ontologies:
            - edam: http://edamontology.org/format_3475 # TSV
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@erikrikarddaniel"
maintainers:
  - "@erikrikarddaniel"
