name: "epang_split"
description: splits an alignment into reference and query parts
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: "https://doi.org/10.1093/sysbio/syy054"
      licence: "['GNU Affero General Public License v3.0']"

input:
  # Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - refaln:
      type: file
      description: reference alignment in any supported format including phylip and fasta, may be gzipped
      pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}"
  - fullaln:
      type: file
      description: full alignment in any supported format to split into reference and query alignments
      pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - query:
      type: file
      description: query sequence alignment in gzipped fasta format
  - reference:
      type: file
      description: reference sequence alignment in gzipped fasta format
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@erikrikarddaniel"
