--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combined.xml	Wed Nov 20 10:00:28 2013 -0500
@@ -0,0 +1,27 @@
+<tool id="immunerepertoirecombined" name="Immunerepertoire combined" version="1.0">
+	<description>pipeline</description>
+	<command interpreter="bash">
+		combined.sh 
+		#for $i, $f in enumerate($files)
+			${f.file}
+			${f.id}
+		#end for
+		$out_file $out_file.files_path
+	</command>
+	<inputs>
+		<repeat name="files" title="File" min="1" default="1">
+			<param name="file" format="fasta" type="data" label="Data to Process" />
+			<param name="id" type="text" label="ID" />
+		</repeat>
+	</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>
+