Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

comparison report_tcell.xml @ 3:b850200d4335 draft

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author davidvanzessen
date Thu, 15 May 2014 09:30:54 -0400
parents 1d429107cd26
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2:fd1b76816395 3:b850200d4335
1 <tool id="report_clonality_t-cells" name="Report Clonality T-Cells" version="1.0"> 1 <tool id="report_clonality_t-cells" name="Report Clonality T-Cells" version="1.0">
2 <description> </description> 2 <description> </description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" "$species" 4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
5 </command> 5 </command>
6 <inputs> 6 <inputs>
7 <param name="in_file" format="tabular" type="data" label="Data to Process" /> 7 <param name="in_file" format="tabular" type="data" label="Data to Process" />
8 <param name="clonaltype_select" type="select" label="Clonal Type Definition"> 8 <param name="clonaltype_select" type="select" label="Clonal Type Definition">
9 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> 9 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
10 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> 10 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
11 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> 11 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
12 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> 12 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
13 <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> 13 <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>
14 </param> 14 </param>
15 <param name="species" type="select" label="Human or Mouse (Does nothing)"> 15
16 <param name="species" type="select" label="Species">
16 <option value="human">Human</option> 17 <option value="human">Human</option>
17 <option value="mouse">Mouse</option> 18 <option value="mouse">Mouse</option>
19 </param>
20
21 <param name="locus" type="select" label="Locus">
22 <option value="trb">TRB</option>
23 <option value="tra">TRA</option>
24 <option value="trg">TRG</option>
25 <option value="trd">TRD</option>
26 </param>
27
28 <param name="selection" type="select" label="Selection">
29 <option value="unique">Unique (Based on clonaltype)</option>
30 <option value="all">All</option>
18 </param> 31 </param>
19 </inputs> 32 </inputs>
20 <outputs> 33 <outputs>
21 <data format="html" name="out_file" /> 34 <data format="html" name="out_file" />
22 </outputs> 35 </outputs>