--- a/mutation_analysis.xml	Thu Apr 16 09:36:19 2015 -0400
+++ b/mutation_analysis.xml	Thu Jun 18 03:10:11 2015 -0400
@@ -1,7 +1,7 @@
 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1}
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -13,6 +13,21 @@
 			<option value="yes">yes</option>
 			<option value="no" selected="true">no</option>
 		</param>
+		<param name="functionality" type="select" label="Functionality filter" help="" >
+			<option value="no_results" selected="true">Remove "No results"</option>
+			<option value="no_result_unproductive">Remove "No results" and "unproductive"</option>
+			<option value="dont_remove">Don't filter</option>
+		</param>
+		
+		<param name="unique" type="select" label="Remove duplicates based on" help="" >
+			<option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option>
+			<option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
+			<option value="V_subclass">V + subclass</option>
+			<option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
+			<option value="AA.JUNCTION">AA.JUNCTION</option>
+			<option value="none">Don't remove duplicates</option>
+		</param>
+		
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>