Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

comparison plotting_merged.xml @ 2:fd1b76816395 draft

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author davidvanzessen
date Thu, 27 Mar 2014 10:54:03 -0400
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1:1ba88ffd6f4e 2:fd1b76816395
1 <tool id="report_clonality_igg" name="Report Clonality" version="1.0">
2 <description> </description>
3 <command interpreter="bash">
4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select"
5 </command>
6 <inputs>
7 <param name="in_file" format="tabular" type="data" label="Data to Process" />
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>
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>
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>
14 </param>
15
16 </inputs>
17 <outputs>
18 <data format="html" name="out_file" />
19 </outputs>
20 <help>
21 Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J)
22 </help>
23 </tool>