--- a/mutation_analysis.xml	Mon Apr 04 04:25:46 2016 -0400
+++ b/mutation_analysis.xml	Wed Apr 06 05:54:13 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
+		wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output $filter_uniques $class_filter
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -19,7 +19,7 @@
 			<option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
 			<option value="dont_filter">Don't filter</option>
 		</param>
-		<param name="filter_uniques" type="select" label="Filter unique sequences">
+		<param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
 			<option value="yes">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
 			<option value="yes_c">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
 			<option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
@@ -33,6 +33,11 @@
 			<option value="AA.JUNCTION">AA.JUNCTION</option>
 			<option value="none">Don't remove duplicates</option>
 		</param>
+		<param name="class_filter" type="select" label="Class/Sublass filter" help="" >
+			<option value="70_70" selected="true">>70% class and >70% subclass</option>
+			<option value="70_0">>70% class</option>
+			<option value="60_0">>60% class</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>
@@ -47,7 +52,28 @@
 		</data>
 	</outputs>
 	<help>
-		Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
+		Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.  
+		
+		+--------------------------+
+		|       unique filter      |
+		+--------+--------+--------+
+		| values | remove | keep   |
+		+--------+--------+--------+
+		|   A    |   A    |   A    |
+		+--------+--------+--------+
+		|   A    |   B    |   B    |
+		+--------+--------+--------+
+		|   B    |   D    |   C    |
+		+--------+--------+--------+
+		|   B    |        |   D    |
+		+--------+--------+--------+
+		|   C    |        |        |
+		+--------+--------+--------+
+		|   D    |        |        |
+		+--------+--------+--------+
+		|   D    |        |        |
+		+--------+--------+--------+
+		
 	</help>
 	<requirements>
     <requirement type="package" version="1.0">blastn</requirement>