Mercurial > repos > davidvanzessen > vidjil_with_browser

comparison vidjil.xml @ 3:e7dc253f92a2 draft

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author davidvanzessen
date Tue, 09 Dec 2014 04:08:17 -0500
parents 7c939eea3dfb
children 786aacc84ac8
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2:7c939eea3dfb 3:e7dc253f92a2
2 <description></description> 2 <description></description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 vidjil.sh $in_file $out_file $out_file.files_path $database $limit_reads $limit_ratio 4 vidjil.sh $in_file $out_file $out_file.files_path $database $limit_reads $limit_ratio
5 </command> 5 </command>
6 <inputs> 6 <inputs>
7 <param name="in_file" type="data" format="fasta" label="Data to Process" /> 7 <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
8 <param name="database" type="select" label="Database"> 8 <param name="database" type="select" label="Database">
9 <option value="current">Germline database from IMGT of 30-9-14</option> 9 <option value="current">Germline database from IMGT of 30-9-14</option>
10 <option value="download">Download newest database from IMGT</option> 10 <option value="download">Download newest database from IMGT</option>
11 </param> 11 </param>
12 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/> 12 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/>
14 </inputs> 14 </inputs>
15 <outputs> 15 <outputs>
16 <data format="html" name="out_file" /> 16 <data format="html" name="out_file" />
17 </outputs> 17 </outputs>
18 <help> 18 <help>
19 A Galaxy wrapper for Vidijl and Vidjil browser 19 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.
20 **Reference** 20
21 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 21 **Reference:**
22 **Website** 22
23 http://bioinfo.lifl.fr/vidjil/ 23 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
24 **Website:**
25
26 http://bioinfo.lifl.fr/vidjil/
24 </help> 27 </help>
25 </tool> 28 </tool>