--- a/shm_csr.xml	Mon Nov 28 05:15:16 2016 -0500
+++ b/shm_csr.xml	Mon Nov 28 07:23:50 2016 -0500
@@ -1,7 +1,7 @@
 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast
+		wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -71,7 +71,7 @@
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 		</data>
-		<data format="imgt_archive" name="naive_output_ca" label = "Naive input data from ${in_file.name}" >
+		<data format="imgt_archive" name="naive_output_all" label = "Naive input data from ${in_file.name}" >
 		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
 		    <filter>class_filter_cond['class_filter'] == "101_101"</filter>
 		</data>

--- a/wrapper.sh	Mon Nov 28 05:15:16 2016 -0500
+++ b/wrapper.sh	Mon Nov 28 07:23:50 2016 -0500
@@ -14,10 +14,11 @@
 naive_output_cg=${10}
 naive_output_cm=${11}
 naive_output_ce=${12}
-filter_unique=${13}
-class_filter=${14}
-empty_region_filter=${15}
-fast=${16}
+naive_output_all=${13}
+filter_unique=${14}
+class_filter=${15}
+empty_region_filter=${16}
+fast=${17}
 mkdir $outdir
 
 tar -xzf $dir/style.tar.gz -C $outdir