<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}
			${f.id}
		#end for
		"$clonaltype_select" $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>
		<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>