--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality_igg.xml	Tue Dec 16 03:33:36 2014 -0500
@@ -0,0 +1,50 @@
+<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" $species $locus $filterproductive
+	</command>
+	<inputs>
+		<param name="in_file" format="tabular" type="data" label="Data to Process" />
+		<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>
+			<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="Species">
+			<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="filterproductive" type="select" label="Filter out the unproductive sequences">
+			<option value="yes">Yes</option>
+			<option value="no">No</option>
+		</param>
+
+	</inputs>
+	<outputs>
+		<data format="html" name="out_file" />
+	</outputs>
+	<help>
+**INPUT**
+
+One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool
+
+**OUTPUT**
+
+It generates the following result:
+	</help>
+</tool>