<tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0">
	<description></description>
	<command interpreter="bash">
		vidjil.sh $in_file $id $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline $fasta_out
	</command>
	<inputs>
		<param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
		<param name="id" type="text" label="ID" />
		<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="selection" type="select" label="Selection">
			<option value="clones">Clones</option>
			<option value="windows">Windows</option>
			<option value="segment">Segment (Not recommended)</option>
			<option value="germlines">Discover all germlines</option>
		</param>
		<param name="germline" type="select" label="Germline">
			<option value="IGH">IGH</option>
			<option value="IGK">IGK</option>
			<option value="TRB">TRB</option>
			<option value="IGH">IGH</option>
			<option value="IGH">IGH</option>
			<option value="IGH">IGH</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" label="Vidjil browser of ${in_file.name}"/>
		<data format="fasta" name="fasta_out" label="Vidjil fasta of ${in_file.name}" />
	</outputs>
	<help>
A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.

**Reference:**

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

**Website:**

http://bioinfo.lifl.fr/vidjil/
	</help>
</tool>