--- a/shm_csr.xml	Mon May 08 09:27:27 2017 -0400
+++ b/shm_csr.xml	Thu May 11 10:21:39 2017 -0400
@@ -1,7 +1,11 @@
 <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_cond.naive_output $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
+		#if str ( $filter_unique.filter_unique_select ) == "remove":
+			wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter $fast
+		#else:
+			wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_unique.filter_unique_select 2 $class_filter_cond.class_filter $empty_region_filter $fast
+		#end if
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
@@ -16,11 +20,16 @@
 			<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" selected="true">Remove uniques (Based on nucleotide sequence + C)</option>
-			<option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
-			<option value="no">No</option>
-		</param>
+        <conditional name="filter_unique">
+			<param name="filter_unique_select" type="select" label="Filter unique sequences" help="See below for an example.">
+				<option value="remove" selected="true">Remove uniques (Based on nucleotide sequence + C)</option>
+				<option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
+				<option value="no">No</option>
+			</param>
+			<when value="remove">
+				<param name="filter_unique_clone_count" size="4" type="integer" label="How many sequences should be in a group to keep 1 of them" value="2" min="2"/>
+			</when>
+		</conditional>
 		<param name="unique" type="select" label="Remove duplicates based on" help="" >
 			<option value="VGene,CDR3.IMGT.AA,best_match_class">Top.V.Gene, CDR3 (AA), C region</option>
 			<option value="VGene,CDR3.IMGT.AA">Top.V.Gene, CDR3 (AA)</option>