Mercurial > repos > davidvanzessen > vidjil_with_browser

comparison vidjil.xml @ 6:7346cd210a43 draft

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author davidvanzessen
date Thu, 12 Feb 2015 09:54:07 -0500
parents b94a4ec63d12
children e55dfd9a8c00
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5:b94a4ec63d12 6:7346cd210a43
1 <tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0"> 1 <tool id="vidjil_galaxy_wrapper" name="Vidjil" version="1.0">
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 "
5 #for $i, $f in enumerate($in_files)
6 ${f.id};${f.in_file}|
7 #end for
8 " $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline
5 </command> 9 </command>
6 <inputs> 10 <inputs>
7 <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" /> 11 <repeat name="in_files" title="Input Files" min="1" default="1">
12 <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
13 <param name="id" type="text" label="ID" />
14 </repeat>
8 <param name="database" type="select" label="Database"> 15 <param name="database" type="select" label="Database">
9 <option value="current">Germline database from IMGT of 30-9-14</option> 16 <option value="current">Germline database from IMGT of 30-9-14</option>
10 <option value="download">Download newest database from IMGT</option> 17 <option value="download">Download newest database from IMGT</option>
18 </param>
19 <param name="selection" type="select" label="Selection">
20 <option value="clones">Clones</option>
21 <option value="windows">Windows</option>
22 <option value="segment">Segment (Not recommended)</option>
23 <option value="germlines">Discover all germlines</option>
24 </param>
25 <param name="germline" type="select" label="Germline">
26 <option value="IGH">IGH</option>
27 <option value="IGK">IGK</option>
28 <option value="TRB">TRB</option>
29 <option value="IGH">IGH</option>
30 <option value="IGH">IGH</option>
31 <option value="IGH">IGH</option>
11 </param> 32 </param>
12 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/> 33 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/>
13 <param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/> 34 <param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/>
14 </inputs> 35 </inputs>
15 <outputs> 36 <outputs>
16 <data format="html" name="out_file" label="Vidjil on ${in_file.name}"/> 37 <data format="html" name="out_file" label="Vidjil on blah"/>
17 </outputs> 38 </outputs>
18 <help> 39 <help>
19 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files. 40 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.
20 41
21 **Reference:** 42 **Reference:**