Mercurial > repos > davidvanzessen > mutation_analysis
diff tmp/baseline/baseline.xml @ 95:a66eb1c5374c draft
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author | davidvanzessen |
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date | Wed, 08 Jun 2016 03:54:49 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tmp/baseline/baseline.xml Wed Jun 08 03:54:49 2016 -0400 @@ -0,0 +1,73 @@ +<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" " + #for $i, $input in enumerate($inputs) + ${input.in_file} + #end for + " + " + #for $i, $input in enumerate($inputs) + ${input.id} + #end for + " + $reference $out_file "$selection" "$out_table" + </command> + <inputs> + <repeat name="inputs" title="inputs" min="1" default="1"> + <param name="in_file" type="data" label="Input excel or IMGT zip file" /> + <param name="id" type="text" label="ID (alpha-numeric, no spaces)" /> + </repeat> + <param name="reference" type="data" format="fasta" label="Reference fasta file" /> + <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="1">Smith DS et al. 1996</option> + <option value="0">Uniform substitution</option> + <option value="5">FiveS</option> + </param> + <param name="mutability" type="select" label="Mutability Model"> + <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option> + <option value="0">Uniform mutability</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="text" value="25:26:38:55:65:104:-" size="40" label="Custom Boundaries (FWR1Start:FWR1End:CDR1End:FWR2End:CDR3End:FWR3End:CDR3End)" /> + <param name="selection" type="select" label="Unique Selection Definition"> + <option value="VGene,AA.JUNCTION">VGene, AA CDR3</option> + <option value="VGene,JGene,AA.JUNCTION">VGene, JGene, AA CDR3</option> + <option value="VGene,DGene,JGene,AA.JUNCTION">VGene, DGene, JGene, AA CDR3</option> + <option value="Sequence.ID">None</option> + </param> + </inputs> + <outputs> + <data format="pdf" name="out_file" label = "Baseline PDF on ${on_string}"/> + <data format="tabular" name="out_table" label = "Baseline Table on ${on_string}"/> + </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. + + **Boundaries** + + IMGT® No CDR3: "1:26:38:55:65:104:-" + + IMGT®: "1:26:38:55:65:104:116" + + </help> +</tool>