--- a/plotting_merged.xml	Thu May 15 09:27:22 2014 -0400
+++ b/plotting_merged.xml	Thu Nov 13 10:33:04 2014 -0500
@@ -1,11 +1,12 @@
 <tool id="report_clonality_igg" name="Report Clonality" version="1.0">
 	<description> </description>
 	<command interpreter="bash">
-		r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
+		r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" $species $locus $filterproductive
 	</command>
 	<inputs>
 		<param name="in_file" format="tabular" type="data" label="Data to Process" />
-		<param name="clonaltype_select" type="select" label="Clonal Type Definition">
+		<param name="clonaltype" type="select" label="Clonal Type Definition">
+			<option value="none">Dont 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>
@@ -17,16 +18,20 @@
 			<option value="human">Human</option>
 			<option value="mouse">Mouse</option>
 		</param>
-		
+
 		<param name="locus" type="select" label="Locus">
 			<option value="igh">IGH</option>
 			<option value="igk">IGK</option>
 			<option value="igl">IGL</option>
+			<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 name="filterproductive" type="select" label="Filter out the unproductive sequences">
+			<option value="yes">Yes</option>
+			<option value="no">No</option>
 		</param>
 
 	</inputs>
@@ -34,6 +39,12 @@
 		<data format="html" name="out_file" />
 	</outputs>
 	<help>
-		Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J)
+**INPUT**
+
+One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool
+
+**OUTPUT**
+
+It generates the following result:
 	</help>
 </tool>