--- a/snippy-core.xml	Fri Jan 18 19:35:46 2019 -0500
+++ b/snippy-core.xml	Fri Jan 18 22:46:34 2019 -0500
@@ -9,14 +9,14 @@
     <command detect_errors="exit_code"><![CDATA[
 
         perl '$__tool_directory__/snippy_core_wrapper.pl'
-            '$is_reference'
+            --ref '$ref'
             --indirs '${" ".join(map(str, $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>
@@ -43,8 +43,8 @@
 
     <tests>
         <test><!-- Test #1 - test with 2 zipped directories -->
-            <param name="indirs" value="S1.tgz,S2.tgz" />
-            <param name="is_reference" value="false" />
+            <param name="indirs" value="S1.tgz,S2.tgz,S3.tgz" />
+            <param name="ref" value="GCF_000293905.1_ASM29390v1_genomic.fna" />
             <param name="outputs" value="outtxt" />
             <output name="alignment_summary" ftype="txt" file="core/core.txt" />
         </test>