Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
comparison baseline.xml @ 0:d685e7ba0ed4 draft
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| author | davidvanzessen |
|---|---|
| date | Tue, 15 Jul 2014 08:43:49 -0400 |
| parents | |
| children | 94fada165724 |
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| -1:000000000000 | 0:d685e7ba0ed4 |
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| 1 <tool id="baseline_bayesian_estimation" name="Baseline" version="1.0"> | |
| 2 <description>Bayesian Estimation of Antigen-Driven Selection</description> | |
| 3 <command interpreter="bash"> | |
| 4 wrapper.sh $ss $species $substitution $mutability $clonal $fixindels "$boundaries" $in_file $out_file.files_path result $out_file $out_file2 | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param name="in_file" format="fasta" type="data" label="Data to Process" /> | |
| 8 <param name="ss" type="select" label="Selection Statistic"> | |
| 9 <option value="1">Focused</option> | |
| 10 <option value="2">Local</option> | |
| 11 </param> | |
| 12 <param name="species" type="select" label="SHM Targeting Model"> | |
| 13 <option value="1">Human</option> | |
| 14 <option value="2">Mouse</option> | |
| 15 </param> | |
| 16 <param name="substitution" type="select" label="Substitution Model"> | |
| 17 <option value="0">Uniform substitution</option> | |
| 18 <option value="1">Smith DS et al. 1996</option> | |
| 19 <option value="5">FiveS</option> | |
| 20 </param> | |
| 21 <param name="mutability" type="select" label="Mutability Model"> | |
| 22 <option value="0">Uniform mutability</option> | |
| 23 <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option> | |
| 24 <option value="5">FiveS</option> | |
| 25 </param> | |
| 26 <param name="clonal" type="select" label="Sequences are clonal"> | |
| 27 <option value="0">Independent sequences</option> | |
| 28 <option value="1">Clonally related</option> | |
| 29 <option value="2">Clonally related and only non-terminal mutations</option> | |
| 30 </param> | |
| 31 <param name="fixindels" type="select" label="Fix Indels"> | |
| 32 <option value="0">Do Nothing</option> | |
| 33 <option value="1">Try and fix Indels</option> | |
| 34 </param> | |
| 35 <param name="boundaries" type="select" label="FWR/CDR3 Boundaries"> | |
| 36 <option value="1:26:38:55:65:104:116">IMGT®</option> | |
| 37 <option value="1:26:38:55:65:104:-">IMGT® No CDR3</option> | |
| 38 </param> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data format="tabular" name="out_file" label = "${tool.name} on ${on_string}: result"/> | |
| 42 <data format="data" name="out_file2" label = "${tool.name} on ${on_string}: RData"/> | |
| 43 </outputs> | |
| 44 <help> | |
| 45 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27. | |
| 46 | |
| 47 Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504. | |
| 48 | |
| 49 </help> | |
| 50 </tool> |