# HG changeset patch
# User davidvanzessen
# Date 1385125966 18000
# Node ID 2b1d3d6843e86209b7f4f02fc6aad8840f05590a
# Parent  bb8d5c67c1294de5e6952c22fc05599fd071d78e
Uploaded

diff -r bb8d5c67c129 -r 2b1d3d6843e8 combined.xml
--- a/combined.xml	Fri Nov 22 08:12:40 2013 -0500
+++ b/combined.xml	Fri Nov 22 08:12:46 2013 -0500
@@ -6,13 +6,20 @@
 			${f.file}
 			${f.id}
 		#end for
-		$out_file $out_file.files_path
+		"$clonaltype_select" $out_file $out_file.files_path
 	</command>
 	<inputs>
 		<repeat name="files" title="File" min="1" default="1">
 			<param name="file" format="fasta" type="data" label="Data to Process" />
 			<param name="id" type="text" label="ID" />
 		</repeat>
+		<param name="clonaltype_select" type="select" label="Clonal Type Definition">
+			<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>
+			<option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
+			<option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
+		</param>
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" />