name: "gappa_examineheattree"
description: colours a phylogeny with placement densities
keywords:
  - phylogeny
  - phylogenetic placement
  - heattree
  - visualisation
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: "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' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - newick:
      type: file
      description: phylogenetic tree file in newick format
      pattern: "*.newick"
  - nexus:
      type: file
      description: coloured phylogenetic tree file in nexus format
      pattern: "*.nexus"
  - phyloxml:
      type: file
      description: coloured phylogenetic tree file in phyloxml format
      pattern: "*.phyloxml"
  - svg:
      type: file
      description: coloured phylogenetic tree file in svg format
      pattern: "*.svg"
  - colours:
      type: file
      description: colours used in plot
      pattern: "*.colours.txt"
  - log:
      type: file
      description: log file from the run
      pattern: "*.log"

authors:
  - "@erikrikarddaniel"
