--- a/mutation_analysis.xml	Fri Mar 25 04:39:18 2016 -0400
+++ b/mutation_analysis.xml	Fri Mar 25 07:50:12 2016 -0400
@@ -19,7 +19,13 @@
 			<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">
+			<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>
+			<option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
+			<option value="no" selected="true">No</option>
+		</param>
 		<param name="unique" type="select" label="Remove duplicates based on" help="" >
 			<option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option>
 			<option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
@@ -33,11 +39,6 @@
 				<option value="no" selected="true">No</option>
 			</param>
 		</conditional>
-		<param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once.">
-			<option value="yes">Yes</option>
-			<option value="no" selected="true">No</option>
-			<option value="keep">Keep uniques and filter out the duplicates</option>
-		</param>
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>