name: hmmer_hmmsearch
description: search profile(s) against a sequence database
keywords:
  - 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 ]
  - hmmfile:
      type: file
      description: One or more HMM profiles created with hmmbuild
      pattern: "*.{hmm,hmm.gz}"
  - seqdb:
      type: file
      description: Database of sequences in FASTA format
      pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}"
  - write_align:
      type: val
      description: Flag to write optional alignment output. Specify with 'true' to output
  - write_target:
      type: val
      description: Flag to write optional per target summary . Specify with 'true' to output
  - write_domain:
      type: val
      description: Flag to write optional per domain summary. Specify with 'true' to output

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - output:
      type: file
      description: Human readable output summarizing hmmsearch results
      pattern: "*.{txt.gz}"
  - alignments:
      type: file
      description: Optional multiple sequence alignment (MSA) in Stockholm format
      pattern: "*.{sto.gz}"
  - target_summary:
      type: file
      description: Optional tabular (space-delimited) summary of per-target output
      pattern: "*.{tbl.gz}"
  - domain_summary:
      type: file
      description: Optional tabular (space-delimited) summary of per-domain output
      pattern: "*.{domtbl.gz}"

authors:
  - "@Midnighter"