--- a/mutation_analysis.xml	Fri Jan 29 05:42:17 2016 -0500
+++ b/mutation_analysis.xml	Fri Jan 29 08:11:31 2016 -0500
@@ -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} $functionality $unique $naive_output
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output $filter_uniques
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -33,6 +33,10 @@
 				<option value="no" selected="true">No</option>
 			</param>
 		</conditional>
+		<param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once.">
+			<option value="yes">Yes</option>
+			<option value="no" selected="true">No</option>
+		</param>
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>