name: "gappa_examineassign"
description: assigns taxonomy to query sequences in phylogenetic placement output
keywords:
  - phylogeny
  - phylogenetic placement
  - classification
  - taxonomy
tools:
  - "gappa":
      description: "Genesis Applications for Phylogenetic Placement Analysis"
      homepage: "https://github.com/lczech/gappa"
      documentation: "https://github.com/lczech/gappa/wiki"
      tool_dev_url: "https://github.com/lczech/gappa"
      doi: "https://doi.org/10.1093/bioinformatics/btaa070"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - jplace:
      type: file
      description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not
      pattern: "*.{jplace,jplace.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - examineassign:
      type: directory
      description: Execution directory
  - profile:
      type: file
      description: profile tsv file
      pattern: "*profile.tsv"
  - labelled_tree:
      type: file
      description: labelled tree in newick format
      pattern: "*labelled_tree.newick"
  - per_query:
      type: file
      description: per query taxonomy assignments in tsv format
      pattern: "*per_query.tsv"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@erikrikarddaniel"