--- a/rapsodyn/PileupVariant.xml	Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/PileupVariant.xml	Mon Jan 19 04:33:21 2015 -0500
@@ -1,10 +1,27 @@
-<tool id="PileupVariant" name="PileupVariant" version="1.01">
+<tool id="PileupVariant" name="PileupVariant" version="1.10">
 <description>Keep only mpileup line with variant</description>
 <command interpreter="perl">
-    PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file 
+  #if $exclude.do=="YES"
+	PileupVariant.pl -input_pileup_file $input_pileup_file -input_exclusion_file $input_exclusion_file -log_file $log_file > $output_pileup_file 
+  #else
+        PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file 
+  #end if
+  
 </command>
 <inputs>
 	<param name="input_pileup_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
+	<conditional name="exclude">
+	  <param name="do" type="select" label="Exclude some position">
+	    <option value="NO">NO</option>
+	    <option value="YES">YES</option>
+	  </param>
+	  <when value="YES">
+		<param name="input_exclusion_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
+	  </when>
+	  <when value="NO">
+	    
+	  </when>
+	</conditional> 
 </inputs>
 <outputs>
 	<data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/>