Mercurial > repos > davidvanzessen > combined_immune_repertoire_imgt

comparison combined_imgt.xml @ 1:d2b3bcabb478 draft

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author davidvanzessen
date Mon, 09 Dec 2013 06:08:52 -0500
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0:e71c59b72669 1:d2b3bcabb478
1 <tool id="immunerepertoirecombined_imgt" name="Immunerepertoire combined" version="1.0">
2 <description>pipeline for IMGT</description>
3 <command interpreter="bash">
4 combined.sh
5 #for $i, $f in enumerate($patients)
6 ${f.id}
7 #for $j, $g in enumerate($f.samples)
8 ${g.sample}
9 #end for
10 #end for
11 "$clonaltype_select" $out_file $out_file.files_path
12 </command>
13 <inputs>
14 <repeat name="patients" title="Patients" min="1" default="1">
15 <repeat name="samples" title="Sample" min="1" default="1">
16 <param name="sample" type="data" label="Sample to Process" />
17 </repeat>
18 <param name="id" type="text" label="ID" />
19 </repeat>
20 <param name="clonaltype_select" type="select" label="Clonal Type Definition">
21 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
22 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
23 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
24 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
25 <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>
26 </param>
27 </inputs>
28 <outputs>
29 <data format="html" name="out_file" />
30 </outputs>
31 <help>
32 The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them.
33 </help>
34 <requirements>
35 <requirement type="package" version="1.0.0">igBlastn</requirement>
36 </requirements>
37 </tool>
38