--- a/rapsodyn/PileupVariant.xml	Mon Sep 29 03:02:16 2014 -0400
+++ b/rapsodyn/PileupVariant.xml	Tue Oct 07 10:34:34 2014 -0400
@@ -1,13 +1,14 @@
-<tool id="PileupVariant" name="PileupVariant" version="0.01">
+<tool id="PileupVariant" name="PileupVariant" version="1.01">
 <description>Keep only mpileup line with variant</description>
 <command interpreter="perl">
-    PileupVariant.pl $input_file > $output_file 
+    PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file 
 </command>
 <inputs>
-<param name="input_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
+	<param name="input_pileup_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
 </inputs>
 <outputs>
- <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/>
+	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>	
 </outputs>
 
 <help>