name: hmmer_hmmalign
description: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile
keywords:
  - alignment
tools:
  - hmmer:
      description: Biosequence analysis using profile hidden Markov models
      homepage: http://hmmer.org/
      documentation: http://hmmer.org/documentation.html
      tool_dev_url: None
      doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195"
      licence: ['BSD']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: Amino acid or nucleotide fasta file, gzipped or not
      pattern: "*.{fna,fna.gz,faa,faa.gz,fasta,fasta.gz,fa,fa.gz}"
  - hmm:
      type: file
      description: HMM file
      pattern: "*.hmm"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - sthlm:
      type: file
      description: Multiple alignment in gzipped Stockholm format
      pattern: "*.sthlm.gz"

authors:
  - "@erikrikarddaniel"