--- a/snippy-core.xml	Tue Mar 12 17:37:29 2019 -0400
+++ b/snippy-core.xml	Mon Jun 17 16:42:39 2019 -0400
@@ -1,3 +1,4 @@
+<?xml version="1.0" encoding="utf-8"?>
 <tool id="snippy_core" name="snippy-core" version="@VERSION@">
     <description>
         Combine multiple Snippy outputs into a core SNP alignment
@@ -7,15 +8,16 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-
-        python '$__tool_directory__/snippy_core_wrapper.py'
+        #for $indir in $indirs
+            tar -xf '$indir' &&
+        #end for
+        snippy-core
             --ref '$ref'
-            --indirs '$indirs'
-
+            `ls -1 -I "*.dat" -I "*.log" | tr '\n' ' '`
     ]]></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="indirs" type="data" multiple="true" format="tar" label="Snippy input zipped dirs" help="Select all the snippy inputs for 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>
@@ -43,10 +45,10 @@
 
     <tests>
         <test><!-- Test #1 - test with 3 zipped directories -->
-            <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
+            <param name="indirs" value="a.dat,b.dat,c.dat" />
             <param name="ref" value="reference.fasta" />
             <param name="outputs" value="outtxt" />
-            <output name="alignment_summary" ftype="txt" file="core/core.txt" />
+            <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
         </test>
     </tests>
 
@@ -71,6 +73,5 @@
 snippy **must** have been run with --cleanup False
 
     ]]></help>
-
     <expand macro="citations" />
 </tool>