<tool id="rnammer" name="rnammer" version="0.1">
  <description>RNAmmer predicts 5S/8S, 16S/18S, and 23S/28S ribosomal RNA in genome sequences.</description>
  <requirements>
    <requirement type="package" version="1.2">rnammer</requirement>
    <requirement type="package" version="2.3.2">hmmer</requirement>
  </requirements>
  <command>rnammer -S $kingdom -m $molecules -xml $out_xml -gff $out_gff -f $out_fasta -h $out_hmm_report
    #if $multi
    -multi
    #end if
    $in_fasta
  </command>
  <inputs>
    <param name="in_fasta" type="data" label="Input sequence (fasta)" help="Genome sequence" />
    <param name="kingdom" type="select" label="Domain" help="Which domain of Life does your sequence belong to." force_select="true" multiple="false" display="radio">
      <option value="arc">Archaea</option>
      <option value="bac" selected="true">Bacteria</option>
      <option value="euk">Eukaryotes</option>
    </param>
    <param name="molecules" type="select" label="Molecules" help="Which rRNAs to detect." force_select="true" multiple="true" display="checkboxes">
      <option value="tsu" selected="true">TSU: 5S/8S</option>
      <option value="ssu" selected="true">SSU: 16S/18S</option>
      <option value="lsu" selected="true">LSU: 23S/28S</option>
    </param>
    <param name="multi" type="boolean" label="Run in parallel?" help="Runs all molecules and both strands in parallel. Require 6 threads." truevalue="true" falsevalue="false" checked="true" />
  </inputs>
  <outputs>
    <data name="out_xml" format="xml" label="rRNA molecules (xml)" />
    <data name="out_gff" format="gff" label="rRNA molecules (GFF)" />
    <data name="out_fasta" format="fasta" label="Predicted rRNA genes (fasta)" />
    <data name="out_hmm_report" format="txt" label="HMM report" />
  </outputs>
  <help>
**What it does**

Runs rnammer, a wrapper that makes use of hmmer to identify ribosomal RNA genes on full or draft genomes. 

**Citation**

Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 2007 Apr 22. 

  </help>
</tool>