--- a/mutation_analysis.xml	Wed Apr 20 10:16:25 2016 -0400
+++ b/mutation_analysis.xml	Fri Apr 22 05:07:10 2016 -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} $functionality $unique $naive_output $filter_uniques $class_filter
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -47,7 +47,13 @@
 	</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}" >
+		<data format="tabular" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
+		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		</data>
+		<data format="tabular" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
+		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		</data>
+		<data format="tabular" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		</data>
 	</outputs>