# HG changeset patch
# User davidvanzessen
# Date 1385124664 18000
# Node ID 2e2a29d505c7fe22c4d005981a0aadf8131166ca
# Parent  a9ad03d52680d8d35fc9388f91123e61b0d16efe
Uploaded

diff -r a9ad03d52680 -r 2e2a29d505c7 plotting_merged.xml
--- a/plotting_merged.xml	Fri Nov 15 04:00:13 2013 -0500
+++ b/plotting_merged.xml	Fri Nov 22 07:51:04 2013 -0500
@@ -1,10 +1,18 @@
 <tool id="plotting_merged" name="Plotting the merged data" version="1.0">
 	<description>Creating a graph of the merged reports.</description>
 	<command interpreter="bash">
-		r_wrapper.sh $in_file $out_file $out_file.files_path
+		r_wrapper.sh $in_file $out_file $out_file.files_path $clonaltype_select
 	</command>
 	<inputs>
-		<param name="in_file" format="tabular" type="data" label="Data to Process" />
+	<param name="in_file" format="tabular" type="data" label="Data to Process" />
+	<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" />