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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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6
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4 vidjil.sh "
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5 #for $i, $f in enumerate($in_files)
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6 ${f.id};${f.in_file}|
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7 #end for
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8 " $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline
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9 </command>
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10 <inputs>
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11 <repeat name="in_files" title="Input Files" min="1" default="1">
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12 <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
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13 <param name="id" type="text" label="ID" />
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14 </repeat>
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15 <param name="database" type="select" label="Database">
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16 <option value="current">Germline database from IMGT of 30-9-14</option>
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17 <option value="download">Download newest database from IMGT</option>
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18 </param>
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19 <param name="selection" type="select" label="Selection">
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20 <option value="clones">Clones</option>
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21 <option value="windows">Windows</option>
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22 <option value="segment">Segment (Not recommended)</option>
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23 <option value="germlines">Discover all germlines</option>
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24 </param>
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25 <param name="germline" type="select" label="Germline">
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26 <option value="IGH">IGH</option>
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27 <option value="IGK">IGK</option>
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28 <option value="TRB">TRB</option>
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29 <option value="IGH">IGH</option>
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30 <option value="IGH">IGH</option>
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31 <option value="IGH">IGH</option>
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32 </param>
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33 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/>
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34 <param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/>
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35 </inputs>
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36 <outputs>
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37 <data format="html" name="out_file" label="Vidjil on blah"/>
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38 </outputs>
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39 <help>
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40 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.
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41
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42 **Reference:**
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43
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44 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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45
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46 **Website:**
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47
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48 http://bioinfo.lifl.fr/vidjil/
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49 </help>
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50 </tool>
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