Mercurial > repos > davidvanzessen > report_clonality_tcell_igg
comparison report_tcell.xml @ 0:1d429107cd26 draft
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| author | davidvanzessen |
|---|---|
| date | Fri, 07 Mar 2014 05:42:31 -0500 |
| parents | |
| children | b850200d4335 |
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| -1:000000000000 | 0:1d429107cd26 |
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| 1 <tool id="report_clonality_t-cells" name="Report Clonality T-Cells" version="1.0"> | |
| 2 <description> </description> | |
| 3 <command interpreter="bash"> | |
| 4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" "$species" | |
| 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 <param name="species" type="select" label="Human or Mouse (Does nothing)"> | |
| 16 <option value="human">Human</option> | |
| 17 <option value="mouse">Mouse</option> | |
| 18 </param> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="html" name="out_file" /> | |
| 22 </outputs> | |
| 23 <help> | |
| 24 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) | |
| 25 </help> | |
| 26 </tool> |