--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnammer.xml	Thu Aug 15 03:29:04 2013 -0400
@@ -0,0 +1,43 @@
+<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>