Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg

comparison complete_immunerepertoire.xml @ 1:778a9d130904 draft

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author davidvanzessen
date Thu, 04 Sep 2014 07:46:23 -0400
parents 7d97fa9a0423
children 0dafe2f9ceb8
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0:7d97fa9a0423 1:778a9d130904
1 <tool id="complete_immunerepertoire_igg" name="Complete ImmuneRepertoire" version="1.0"> 1 <tool id="complete_immunerepertoire_igg" name="Complete ImmuneRepertoire" version="1.0">
2 <description> </description> 2 <description> </description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 complete.sh 4 complete.sh "
5 #for $i, $f in enumerate($patients) 5 #for $i, $f in enumerate($patients)
6 ${f.id} 6 ${f.id}
7 #for $j, $g in enumerate($f.samples) 7 #for $j, $g in enumerate($f.samples)
8 ${g.sample} 8 ${g.sample}
9 #end for 9 #end for
10 #end for 10 #end for
11 "$clonaltype_select" $out_file $out_file.files_path $species $locus $selection 11 " $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <repeat name="patients" title="Patients" min="1" default="1"> 14 <repeat name="patients" title="Patients" min="1" default="1">
15 <repeat name="samples" title="Sample" min="1" default="1"> 15 <repeat name="samples" title="Sample" min="1" default="1">
16 <param name="sample" type="data" label="Sample to Process" /> 16 <param name="sample" type="data" label="Sample to Process" />
17 </repeat> 17 </repeat>
18 <param name="id" type="text" label="ID" /> 18 <param name="id" type="text" label="ID" />
19 </repeat> 19 </repeat>
20 <param name="clonaltype_select" type="select" label="Clonal Type Definition"> 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> 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> 22 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
32 32
33 <param name="locus" type="select" label="Locus"> 33 <param name="locus" type="select" label="Locus">
34 <option value="igh">IGH</option> 34 <option value="igh">IGH</option>
35 <option value="igk">IGK</option> 35 <option value="igk">IGK</option>
36 <option value="igl">IGL</option> 36 <option value="igl">IGL</option>
37 <option value="trb">TRB</option>
38 <option value="tra">TRA</option>
39 <option value="trg">TRG</option>
40 <option value="trd">TRD</option>
37 </param> 41 </param>
38 42
39 <param name="selection" type="select" label="Selection"> 43 <param name="selection" type="select" label="Selection">
40 <option value="unique">Unique (Based on clonaltype)</option> 44 <option value="unique">Unique (Based on clonaltype)</option>
41 <option value="all">All</option> 45 <option value="all">All</option>