--- a/roary.xml	Sun Jan 19 04:37:17 2020 -0500
+++ b/roary.xml	Mon Jun 29 08:40:27 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="roary" name="Roary" version="3.13.0">
+<tool id="roary" name="Roary" version="3.13.0+galaxy0">
     <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
 
     <requirements>
@@ -63,6 +63,7 @@
         <option value="numpangene_rtab">Number of Genes in Pan Genome in Rtab format</option>
         <option value="numnew_rtab">Number of New Genes in Rtab format</option>
         <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option>
+        <option value="pangenomeref">FASTA file which contains a single representative nucleotide sequence from each of the clusters in the pan genome (core and accessory)</option>
       </param>
 
       <section name="advanced" title="Advanced options" expanded="false">
@@ -123,6 +124,9 @@
       <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab" >
         <filter>outputs and 'numuniq_rtab' in outputs</filter>
       </data>
+      <data format="fasta" name="pan_genome_ref" label="${tool.name} on ${on_string} pan-genome reference" from_work_dir="out/pan_genome_reference.fa" >
+        <filter>outputs and 'pangenomeref' in outputs</filter>
+      </data>
     </outputs>
 
     <tests>