--- a/snippy-core.xml	Sun Dec 01 13:06:05 2019 -0500
+++ b/snippy-core.xml	Mon Jan 27 21:50:49 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy1">
+<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy2">
     <description>
         Combine multiple Snippy outputs into a core SNP alignment
     </description>
@@ -9,14 +9,14 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @REFERENCE_SOURCE_FILE@
+        mkdir 'snippy_dirs' && cd 'snippy_dirs' &&
         #for $indir in $indirs
-            #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
-            mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
+            tar -xf '$indir' -C . &&
         #end for
-        #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs])
+        cd - &&
         snippy-core
             @REFERENCE_COMMAND@
-            ${snippy_dirs}
+            snippy_dirs/*
     ]]></command>
 
     <inputs>