--- a/shm_csr.xml	Thu Oct 13 10:52:24 2016 -0400
+++ b/shm_csr.xml	Tue Oct 25 07:28:43 2016 -0400
@@ -1,24 +1,20 @@
 <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} ${include_fr1} $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
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
 		<param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
+			<option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
 			<option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
 			<option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
 			<option value="FR2">FR2: include CDR2,FR3 in filters</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>
 		<param name="functionality" type="select" label="Functionality filter" help="" >
-			<option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option>
-			<option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
-			<option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
-			<option value="dont_filter">Don't filter</option>
+			<option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
+			<option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option>
+			<option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>
 		</param>
 		<param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
 			<option value="remove">Remove uniques (Based on nucleotide sequence + C)</option>
@@ -42,7 +38,7 @@
 			<option value="60_55">>60% class and >55% subclass</option>
 			<option value="70_0">>70% class</option>
 			<option value="60_0">>60% class</option>
-			<option value="101_101">No class</option>
+			<option value="101_101">Do not assign (sub)class</option>
 		</param>
 		<conditional name="naive_output_cond">
 			<param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">