--- a/mutation_analysis.xml	Thu Nov 05 10:16:32 2015 -0500
+++ b/mutation_analysis.xml	Mon Nov 09 07:21:09 2015 -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
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -27,10 +27,18 @@
 			<option value="AA.JUNCTION">AA.JUNCTION</option>
 			<option value="none">Don't remove duplicates</option>
 		</param>
-		
+		<conditional name="naive_output_cond">
+			<param name="naive_output" type="select" label="Output a file for naive analysis?">
+				<option value="yes">Yes</option>
+				<option value="no" selected="true">No</option>
+			</param>
+		</conditional>
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
+		<data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" >
+		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		</data>
 	</outputs>
 	<help>
 		Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.