--- a/complete_immunerepertoire.xml	Mon Sep 08 04:24:04 2014 -0400
+++ b/complete_immunerepertoire.xml	Mon Jan 05 09:30:08 2015 -0500
@@ -8,7 +8,7 @@
  ${g.sample}
             #end for
 		#end for
-" $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
+" $out_file $out_file.files_path "$clonaltype" $species $locus $filterproductive
 	</command>
 	<inputs>
 		<repeat name="patients" title="Patients" min="1" default="1">
@@ -17,7 +17,8 @@
 			</repeat>
 			<param name="id" type="text" label="ID" />
 		</repeat>
-		<param name="clonaltype_select" type="select" label="Clonal Type Definition">
+		<param name="clonaltype" type="select" label="Clonal Type Definition">
+			<option value="none">Don't remove duplicates based on clonaltype</option>
 			<option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
 			<option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
 			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
@@ -39,10 +40,10 @@
 			<option value="trg">TRG</option>
 			<option value="trd">TRD</option>
 		</param>
-
-		<param name="selection" type="select" label="Selection">
-			<option value="unique">Unique (Based on clonaltype)</option>
-			<option value="all">All</option>
+		
+		<param name="filterproductive" type="select" label="Filter out the unproductive sequences">
+			<option value="yes">Yes</option>
+			<option value="no">No</option>
 		</param>
 	</inputs>
 	<outputs>
@@ -52,4 +53,3 @@
 		The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them.
 	</help>
 </tool>
-