--- a/snippy-core.xml	Thu Jan 24 14:19:32 2019 -0500
+++ b/snippy-core.xml	Fri Mar 08 20:46:56 2019 -0500
@@ -8,15 +8,15 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        perl '$__tool_directory__/snippy_core_wrapper.pl'
-            '$is_reference'
-            --indirs '${" ".join(map(str, $indirs))}'
+        python '$__tool_directory__/snippy_core_wrapper.py'
+            --ref '$ref'
+            --indirs '$indirs'
 
     ]]></command>
 
     <inputs>
         <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
-        <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." />
+        <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
         <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
             <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
             <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
@@ -42,9 +42,9 @@
     </outputs>
 
     <tests>
-        <test><!-- Test #1 - test with 2 zipped directories -->
-            <param name="indirs" value="S1.tgz,S2.tgz" />
-            <param name="is_reference" value="false" />
+        <test><!-- Test #1 - test with 3 zipped directories -->
+            <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
+            <param name="ref" value="reference.fasta" />
             <param name="outputs" value="outtxt" />
             <output name="alignment_summary" ftype="txt" file="core/core.txt" />
         </test>