--- a/mutation_analysis.xml	Thu Apr 02 03:31:23 2015 -0400
+++ b/mutation_analysis.xml	Tue Apr 07 03:52:34 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}
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1}
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -9,6 +9,10 @@
 			<option value="custom" selected="true">custom</option>
 			<option value="blastn">blastn</option>
 		</param>
+		<param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
+			<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}"/>