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"]
      identifier: ""
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}"
        ontologies: []
    - seqdb:
        type: file
        description: Database of sequences in FASTA format
        pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}"
        ontologies: []
    - write_align:
        type: boolean
        description: Flag to save optional alignment output. Specify with 'true' to
          save.
    - write_target:
        type: boolean
        description: Flag to save optional per target summary. Specify with 'true' to
          save.
    - write_domain:
        type: boolean
        description: Flag to save optional per domain summary. Specify with 'true' to
          save.
output:
  output:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.txt.gz":
          type: file
          description: Human readable output summarizing hmmsearch results
          pattern: "*.{txt.gz}"
          ontologies: []
  alignments:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.sto.gz":
          type: file
          description: Optional multiple sequence alignment (MSA) in Stockholm format
          pattern: "*.{sto.gz}"
          ontologies: []
  target_summary:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.tbl.gz":
          type: file
          description: Optional tabular (space-delimited) summary of per-target output
          pattern: "*.{tbl.gz}"
          ontologies: []
  domain_summary:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.domtbl.gz":
          type: file
          description: Optional tabular (space-delimited) summary of per-domain output
          pattern: "*.{domtbl.gz}"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@Midnighter"
maintainers:
  - "@Midnighter"
