Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison combined.xml @ 3:2b1d3d6843e8 draft

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author davidvanzessen
date Fri, 22 Nov 2013 08:12:46 -0500
parents 4e3df2384422
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2:bb8d5c67c129 3:2b1d3d6843e8
4 combined.sh 4 combined.sh
5 #for $i, $f in enumerate($files) 5 #for $i, $f in enumerate($files)
6 ${f.file} 6 ${f.file}
7 ${f.id} 7 ${f.id}
8 #end for 8 #end for
9 $out_file $out_file.files_path 9 "$clonaltype_select" $out_file $out_file.files_path
10 </command> 10 </command>
11 <inputs> 11 <inputs>
12 <repeat name="files" title="File" min="1" default="1"> 12 <repeat name="files" title="File" min="1" default="1">
13 <param name="file" format="fasta" type="data" label="Data to Process" /> 13 <param name="file" format="fasta" type="data" label="Data to Process" />
14 <param name="id" type="text" label="ID" /> 14 <param name="id" type="text" label="ID" />
15 </repeat> 15 </repeat>
16 <param name="clonaltype_select" type="select" label="Clonal Type Definition">
17 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
18 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
19 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
20 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
21 <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
22 </param>
16 </inputs> 23 </inputs>
17 <outputs> 24 <outputs>
18 <data format="html" name="out_file" /> 25 <data format="html" name="out_file" />
19 </outputs> 26 </outputs>
20 <help> 27 <help>