--- a/shm_csr.xml	Mon Oct 31 05:05:26 2016 -0400
+++ b/shm_csr.xml	Tue Nov 01 10:15:37 2016 -0400
@@ -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 $filter_uniques $class_filter $empty_region_filter
+		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 $filter_uniques $class_filter $empty_region_filter $fast
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -33,7 +33,7 @@
 			<option value="CDR3.IMGT.seq">CDR3 (nt)</option>
 			<option value="Sequence.ID">Don't remove duplicates</option>
 		</param>
-		<param name="class_filter" type="select" label="Class/Subclass filter" help="" >
+		<param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
 			<option value="70_70" selected="true">>70% class and >70% subclass</option>
 			<option value="60_55">>60% class and >55% subclass</option>
 			<option value="70_0">>70% class</option>
@@ -46,6 +46,14 @@
 				<option value="no" selected="true">No</option>
 			</param>
 		</conditional>
+		
+		
+		<param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" >
+			<option value="yes">Yes</option>
+			<option value="no" selected="true">No</option>
+		</param>
+		
+		
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>