Mercurial > repos > davidvanzessen > vidjil_with_browser

comparison vidjil.xml @ 7:e55dfd9a8c00 draft default tip

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author davidvanzessen
date Thu, 12 Feb 2015 10:47:15 -0500
parents 7346cd210a43
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6:7346cd210a43 7:e55dfd9a8c00
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 " 4 vidjil.sh $in_file $id $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline $fasta_out
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
9 </command> 5 </command>
10 <inputs> 6 <inputs>
11 <repeat name="in_files" title="Input Files" min="1" default="1"> 7 <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" />
12 <param name="in_file" type="data" format="fasta,fastq" label="Data to Process" /> 8 <param name="id" type="text" label="ID" />
13 <param name="id" type="text" label="ID" />
14 </repeat>
15 <param name="database" type="select" label="Database"> 9 <param name="database" type="select" label="Database">
16 <option value="current">Germline database from IMGT of 30-9-14</option> 10 <option value="current">Germline database from IMGT of 30-9-14</option>
17 <option value="download">Download newest database from IMGT</option> 11 <option value="download">Download newest database from IMGT</option>
18 </param> 12 </param>
19 <param name="selection" type="select" label="Selection"> 13 <param name="selection" type="select" label="Selection">
32 </param> 26 </param>
33 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/> 27 <param name="limit_reads" type="text" label="Minimal number of reads supporting a clone" value='10'/>
34 <param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/> 28 <param name="limit_ratio" type="text" label="Minimal percentage of reads supporting a clone" value='0'/>
35 </inputs> 29 </inputs>
36 <outputs> 30 <outputs>
37 <data format="html" name="out_file" label="Vidjil on blah"/> 31 <data format="html" name="out_file" label="Vidjil browser of ${in_file.name}"/>
32 <data format="fasta" name="fasta_out" label="Vidjil fasta of ${in_file.name}" />
38 </outputs> 33 </outputs>
39 <help> 34 <help>
40 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files. 35 A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.
41 36
42 **Reference:** 37 **Reference:**