Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
diff baseline.xml @ 0:d685e7ba0ed4 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 15 Jul 2014 08:43:49 -0400 |
| parents | |
| children | 94fada165724 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/baseline.xml Tue Jul 15 08:43:49 2014 -0400 @@ -0,0 +1,50 @@ +<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>