<tool id="baseline_fasta_generator" name="Baseline generator" version="1.0">
	<description>Generate baseline fasta file</description>
	<command interpreter="bash">
		wrapper.sh $in_file $reference $out_file
	</command>
	<inputs>
		<param name="in_file" type="data" label="Input excel file" />
		<param name="reference" type="data" format="fasta" label="Reference fasta file" />
	</inputs>
	<outputs>
		<data format="fasta" name="out_file" label = "Baseline generator on $in_file.name 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>