# HG changeset patch
# User davidvanzessen
# Date 1453909298 18000
# Node ID 188712b1735fe02e4b75509c6b8e90f72ab4afab
# Parent  d08dfc8d52253691af1a23aa75c1fa72c2ea26f5
Uploaded

diff -r d08dfc8d5225 -r 188712b1735f complete_immunerepertoire.xml
--- a/complete_immunerepertoire.xml	Wed Jan 27 10:36:35 2016 -0500
+++ b/complete_immunerepertoire.xml	Wed Jan 27 10:41:38 2016 -0500
@@ -10,9 +10,9 @@
 #end for
 " $out_file $out_file.files_path "$clonaltype"
 #if $gene_selection.source == "imgtdb"		
-	"${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method
+	"${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method $filter_uniques
 #else
-	"custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
+	"custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method $filter_uniques
 #end if
 	</command>
 	<inputs>
@@ -107,6 +107,11 @@
 			<option value="old">Old</option>
 			<option value="boyd">R Package</option>
 		</param>
+		
+		<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">No</option>
+		</param>
 
 	</inputs>
 	<outputs>