Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
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author | davidvanzessen |
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date | Tue, 15 Jul 2014 09:00:24 -0400 |
parents | d685e7ba0ed4 |
children | 94fada165724 |
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<tool id="baseline_bayesian_estimation" name="Baseline" version="1.0"> <description>Bayesian Estimation of Antigen-Driven Selection</description> <command interpreter="bash"> wrapper.sh $ss $species $substitution $mutability $clonal $fixindels "$boundaries" $in_file $out_file.files_path result $out_file $out_file2 </command> <inputs> <param name="in_file" format="fasta" type="data" label="Data to Process" /> <param name="ss" type="select" label="Selection Statistic"> <option value="1">Focused</option> <option value="2">Local</option> </param> <param name="species" type="select" label="SHM Targeting Model"> <option value="1">Human</option> <option value="2">Mouse</option> </param> <param name="substitution" type="select" label="Substitution Model"> <option value="0">Uniform substitution</option> <option value="1">Smith DS et al. 1996</option> <option value="5">FiveS</option> </param> <param name="mutability" type="select" label="Mutability Model"> <option value="0">Uniform mutability</option> <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option> <option value="5">FiveS</option> </param> <param name="clonal" type="select" label="Sequences are clonal"> <option value="0">Independent sequences</option> <option value="1">Clonally related</option> <option value="2">Clonally related and only non-terminal mutations</option> </param> <param name="fixindels" type="select" label="Fix Indels"> <option value="0">Do Nothing</option> <option value="1">Try and fix Indels</option> </param> <param name="boundaries" type="select" label="FWR/CDR3 Boundaries"> <option value="1:26:38:55:65:104:116">IMGT®</option> <option value="1:26:38:55:65:104:-">IMGT® No CDR3</option> </param> </inputs> <outputs> <data format="tabular" name="out_file" label = "${tool.name} on ${on_string}: result"/> <data format="data" name="out_file2" label = "${tool.name} on ${on_string}: RData"/> </outputs> <help> Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27. 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. </help> </tool>