--- a/barrnap.xml	Mon Aug 28 14:14:10 2017 -0400
+++ b/barrnap.xml	Sun Jun 10 03:26:32 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="barrnap" name="barrnap" version="1.2.0">
+<tool id="barrnap" name="barrnap" version="1.2.1">
     <description>Locate ribosomal RNA's in a fasta file. (GFF output)</description>
     <requirements>
-        <requirement type="package" version="0.8">barrnap</requirement>
+        <requirement type="package" version="0.9">barrnap</requirement>
     </requirements>
     <version_command>barrnap --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -14,6 +14,9 @@
         #if $incseq
             --incseq
         #end if
+        #if $outseq
+            --outseq '$fasta_out'
+        #end if
         --kingdom $kingdom
         '$fasta_file'
         > '$gff'
@@ -32,10 +35,14 @@
         <param name="lencutoff" type="float" value="0.8" label="Length cutoff" help="Proportional length threshold to tag a find as pseudo" />
         <param name="evalue" type="float" value="1e-06" label="e-value" help="Similarity e-value cutoff" />
         <param name="incseq" type="boolean" label="Include Sequences in GFF" help="Include the fasta sequences in the GFF output file" />
+        <param name="outseq" type="boolean" label="Save rRNA hit seqs as FASTA" help="Produce an output file of the rRNA sequences found in FASTA format." />
     </inputs>
 
     <outputs>
         <data name="gff" format="gff3" label="${tool.name} on ${on_string}: rRNA GFF"/>
+        <data name="fasta_out" format="fasta" label="${tool.name} on ${on_string}: rRNA Sequences">
+            <filter>outseq</filter>
+        </data>
     </outputs>
 
     <tests>
@@ -56,6 +63,13 @@
             <param name="evalue" value="0.00000001" />
             <output name="gff" value="test_3.gff" ftype="gff3" />
         </test>
+        <test><!-- Test 4 -->
+            <param name="fasta_file" value="small.fna" ftype="fasta" />
+            <param name="outseq" value="true" />
+            <param name="kingdom" value="bac" />
+            <output name="gff" value="test_4.gff" ftype="gff3" />
+            <output name="fasta_out" value="test_4.fna" ftype="fasta" />
+        </test>
     </tests>
 
 <help>