<tool id="imgt_immunerepertoire_igg" name="IMGT ImmuneRepertoire" version="1.0">
	<description> </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 IMGT zip files, give them an ID and it will parse, merge and plot them.
	</help>
</tool>