name: "hmmer_hmmbuild"
description: create an hmm profile from a multiple sequence alignment
keywords:
  - search
  - hidden Markov model
  - HMM
  - hmmer
  - hmmsearch
tools:
  - "hmmer":
      description: "Biosequence analysis using profile hidden Markov models"
      homepage: "http://hmmer.org"
      documentation: "http://hmmer.org/documentation.html"
      tool_dev_url: "https://github.com/EddyRivasLab/hmmer"
      doi: "10.1371/journal.pcbi.1002195"
      licence: "['BSD']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - alignment:
      type: file
      description: multiple sequence alignment in fasta, clustal, stockholm or phylip format
      pattern: "*"
  - mxfile:
      type: file
      description: read substitution score matrix, for use when building profiles from single sequences (--singlemx option)
      pattern: "*"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - hmm:
      type: file
      description: Gzipped HMM file
      pattern: "*.{hmm.gz}"

authors:
  - "@erikrikarddaniel"