<tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0">
	<description></description>
	<command interpreter="bash">
		vidjil.sh $in_file $out_file $out_file.files_path $database $limit_reads $limit_ratio
	</command>
	<inputs>
		<param name="in_file" type="data" format="fasta" label="Data to Process" />
		<param name="database" type="select" label="Database">
			<option value="current">Germline database from IMGT of 30-9-14</option>
			<option value="download">Download newest database from IMGT</option>
		</param>
		<param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/>
		<param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/>
	</inputs>
	<outputs>
		<data format="html" name="out_file" />
	</outputs>
	<help>
		A Galaxy wrapper for Vidijl and Vidjil browser: <br />
		Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, Aurélie Caillault, Nathalie Grardel, Christophe Roumier, Claude Preudhomme, Martin Figeac, Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing, BMC Genomics, 15:409, doi:10.1186/1471-2164-15-409  <br />
		<br />
		http://bioinfo.lifl.fr/vidjil/
	</help>
</tool>