--- a/report_tcell.xml	Thu Mar 27 10:54:03 2014 -0400
+++ b/report_tcell.xml	Thu May 15 09:30:54 2014 -0400
@@ -1,7 +1,7 @@
 <tool id="report_clonality_t-cells" name="Report Clonality T-Cells" version="1.0">
 	<description> </description>
 	<command interpreter="bash">
-		r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" "$species"
+		r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
 	</command>
 	<inputs>
 	<param name="in_file" format="tabular" type="data" label="Data to Process" />
@@ -12,10 +12,23 @@
 		<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>
-	<param name="species" type="select" label="Human or Mouse (Does nothing)">
+
+	<param name="species" type="select" label="Species">
 		<option value="human">Human</option>
 		<option value="mouse">Mouse</option>
 	</param>
+
+	<param name="locus" type="select" label="Locus">
+		<option value="trb">TRB</option>
+		<option value="tra">TRA</option>
+		<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>
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" />