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1 <tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0">
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2 <description></description>
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3 <command interpreter="bash">
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7
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4 vidjil.sh $in_file $id $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline $fasta_out
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5 </command>
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6 <inputs>
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7
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7 <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
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8 <param name="id" type="text" label="ID" />
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9 <param name="database" type="select" label="Database">
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10 <option value="current">Germline database from IMGT of 30-9-14</option>
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11 <option value="download">Download newest database from IMGT</option>
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12 </param>
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13 <param name="selection" type="select" label="Selection">
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14 <option value="clones">Clones</option>
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15 <option value="windows">Windows</option>
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16 <option value="segment">Segment (Not recommended)</option>
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17 <option value="germlines">Discover all germlines</option>
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18 </param>
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19 <param name="germline" type="select" label="Germline">
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20 <option value="IGH">IGH</option>
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21 <option value="IGK">IGK</option>
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22 <option value="TRB">TRB</option>
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23 <option value="IGH">IGH</option>
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24 <option value="IGH">IGH</option>
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25 <option value="IGH">IGH</option>
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26 </param>
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27 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/>
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28 <param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/>
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29 </inputs>
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30 <outputs>
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31 <data format="html" name="out_file" label="Vidjil browser of ${in_file.name}"/>
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32 <data format="fasta" name="fasta_out" label="Vidjil fasta of ${in_file.name}" />
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33 </outputs>
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34 <help>
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35 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.
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36
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37 **Reference:**
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38
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39 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
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4
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40
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41 **Website:**
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42
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43 http://bioinfo.lifl.fr/vidjil/
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44 </help>
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45 </tool>
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