name: "epang_place"
description: phylogenetic placement of query sequences in a reference tree
keywords:
  - phylogeny
  - phylogenetic placement
  - sequences
tools:
  - "epang":
      description: "Massively parallel phylogenetic placement of genetic sequences"
      homepage: "https://github.com/Pbdas/epa-ng"
      documentation: "https://github.com/Pbdas/epa-ng/wiki/Full-Stack-Example"
      tool_dev_url: "https://github.com/Pbdas/epa-ng"
      doi: "10.1093/sysbio/syy054"
      licence: "['GNU Affero General Public License v3.0']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - queryaln:
      type: file
      description: aligned query sequences in any supported format including phylip and fasta, may be gzipped
      pattern: "*"
  - referencealn:
      type: file
      description: reference alignment in any supported format including phylip and fasta, may be gzipped
      pattern: "*"
  - referencetree:
      type: file
      description: newick file containing the reference tree in which query sequences will be placed
      pattern: "*"
  - bfastfile:
      type: file
      description: file argument to the --bfast parameter
      pattern: "*"
  - binaryfile:
      type: file
      description: file argument to the --binary parameter
      pattern: "*"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - epang:
      type: directory
      description: directory in which EPA-NG was run
  - jplace:
      type: file
      description: gzipped file with placement information
      pattern: "*.jplace.gz"
  - log:
      type: file
      description: log file from placement
      pattern: "*.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@erikrikarddaniel"
