<tool id="from_imgt_clonal_pairs" name="IMGT to Paired Clonal Sequences" version="1.0">
	<description>Comparison of clonal sequences in paired samples</description>
	<command interpreter="bash">
from_imgt.sh $out_file
	#for $i, $f in enumerate($patients)
"$f.name" "$f.cellcount" "$f.receptor" "$len($f.samples)"
		#for $j, $g in enumerate($f.samples)
"${g.sname}" "${g.file}" 
		#end for
	#end for
	</command>
	<inputs>
	<repeat name="patients" title="Patient" min="1" default="1">
			<param name="name" type="text" label="Patient name" />
			<param name="cellcount" type="text" label="Cell Count" />
			<param name="receptor" type="text" label="Receptor" />
			<repeat name="samples" title="Sample" min="1" max="2" default="1">
				<param name="sname" type="text" label="Sample name" />
				<param name="file" type="data" label="Data to Process" />
			</repeat>
	</repeat>

	</inputs>
	<outputs>
		<data format="tabular" name="out_file" />
	</outputs>
	<help>
	</help>
</tool>