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<tool id="baseline_fasta_generator" name="Baseline generator" version="1.0">
	<description>Generate baseline fasta file</description>
	<command interpreter="bash">
		wrapper.sh "
		#for $i, $input in enumerate($inputs)
 ${input.in_file}
		#end for 
		"
		"
		#for $i, $input in enumerate($inputs)
 ${input.id}
		#end for 
		"
    $reference $out_file
	</command>
	<inputs>
		<repeat name="inputs" title="inputs" min="1" default="1">
			<param name="in_file" type="data" label="Input excel or IMGT zip file" />
			<param name="id" type="text" label="ID (alpha-numeric, no spaces)" />
		</repeat>
		<param name="reference" type="data" format="fasta" label="Reference fasta file" />
	</inputs>
	<outputs>
		<data format="fasta" name="out_file" label = "Baseline generator on ${on_string} with $reference.name"/>
	</outputs>
	<help>
			Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.

			Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504.
	</help>
</tool>