--- a/complete_immunerepertoire.xml	Tue Aug 02 09:05:44 2016 -0400
+++ b/complete_immunerepertoire.xml	Mon Aug 08 08:53:33 2016 -0400
@@ -10,13 +10,13 @@
 #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 ${clonality_method}
 #else
 	"custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
 #end if
 	</command>
 	<inputs>
-		<repeat name="patients" title="Patients" min="1" default="1">
+		<repeat name="patients" title="Donor" min="1" default="1">
 			<repeat name="samples" title="Sample" min="1" default="1">
 					<param name="sample" type="data" label="Sample to Process" />
 			</repeat>
@@ -32,7 +32,7 @@
 		</param>
 		
 		<conditional name="gene_selection" >
-			<param name="source" type="select" label="Gene reference" help="" >
+			<param name="source" type="select" label="Order of V(D)J genes in graphs" help="" >
 					<option value="imgtdb" selected="true">IMGT-DB</option>
 					<option value="custom">User defined</option>
 			</param>
@@ -98,16 +98,15 @@
 			</when>
 		</conditional>
 		
-		<param name="filterproductive" type="select" label="Filter out the unproductive sequences">
+		<param name="filterproductive" type="select" label="Remove the unproductive sequences from graphs ">
 			<option value="yes">Yes</option>
 			<option value="no">No</option>
 		</param>
-
+		
 		<param name="clonality_method" type="select" label="Old clonality algorithm or the newer R package">
 			<option value="old">Old</option>
-			<option value="boyd">R Package</option>
+			<option value="boyd">R Package (needs 3 replicate minimum)</option>
 		</param>
-
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" />