--- a/snippy-core.xml	Fri Jun 21 14:38:05 2019 -0400
+++ b/snippy-core.xml	Sat Jan 25 00:00:54 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy3">
+<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy1">
     <description>
         Combine multiple Snippy outputs into a core SNP alignment
     </description>
@@ -8,17 +8,20 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+        @REFERENCE_SOURCE_FILE@
         #for $indir in $indirs
-            tar -xf '$indir' &&
+            #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
+            mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
         #end for
+        #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs])
         snippy-core
-            --ref '$ref'
-            `ls -1 -I "*.dat" -I "*.log" | tr '\n' ' '`
+            @REFERENCE_COMMAND@
+            ${snippy_dirs}
     ]]></command>
 
     <inputs>
-        <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="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
+        <expand macro="reference_selector" />
         <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>
@@ -38,7 +41,7 @@
         <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab">
             <filter>outputs and 'outtab' in outputs</filter>
         </data>
-        <data format="tabular" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt">
+        <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt">
             <filter>outputs and 'outtxt' in outputs</filter>
         </data>
     </outputs>
@@ -46,9 +49,21 @@
     <tests>
         <test><!-- Test #1 - test with 3 zipped directories -->
             <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
-            <param name="ref" value="reference.fasta" />
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history"/>
+                <param name="ref_file" value="reference.fasta" ftype="fasta"/>
+            </conditional>
             <param name="outputs" value="outtxt" />
-            <output name="alignment_summary" ftype="tabular" file="a_b_c.core.txt" />
+            <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
+        </test>
+        <test><!-- Test #2 - test with 3 zipped directories -->
+            <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="test_id"/>
+            </conditional>
+            <param name="outputs" value="outtxt" />
+            <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
         </test>
     </tests>