--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combined_imgt.xml	Mon Dec 09 06:08:52 2013 -0500
@@ -0,0 +1,38 @@
+<tool id="immunerepertoirecombined_imgt" name="Immunerepertoire combined" version="1.0">
+	<description>pipeline for IMGT</description>
+	<command interpreter="bash">
+		combined.sh
+		#for $i, $f in enumerate($patients)
+			${f.id}
+            #for $j, $g in enumerate($f.samples)
+            	${g.sample}
+            #end for
+		#end for
+		"$clonaltype_select" $out_file $out_file.files_path
+	</command>
+	<inputs>
+		<repeat name="patients" title="Patients" min="1" default="1">
+            <repeat name="samples" title="Sample" min="1" default="1">
+                <param name="sample" type="data" label="Sample to Process" />
+            </repeat>
+			<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" />
+	</outputs>
+	<help>
+		The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them.
+	</help>
+	<requirements>
+		<requirement type="package" version="1.0.0">igBlastn</requirement>
+	</requirements>
+</tool>
+