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"]
      identifier: ""
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: "*"
        ontologies: []
  - mxfile:
      type: file
      description: read substitution score matrix, for use when building profiles from
        single sequences (--singlemx option)
      pattern: "*"
      ontologies: []
output:
  hmm:
    - - meta:
          type: file
          description: Gzipped HMM file
          pattern: "*.{hmm.gz}"
          ontologies: []
      - "*.hmm.gz":
          type: file
          description: Gzipped HMM file
          pattern: "*.{hmm.gz}"
          ontologies: []
  hmmbuildout:
    - "*.hmmbuild.txt":
        type: file
        description: HMM build output
        ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@erikrikarddaniel"
maintainers:
  - "@erikrikarddaniel"
