Mercurial > repos > davidvanzessen > mutation_analysis
comparison 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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| 94:e39176ccddc8 | 95:a66eb1c5374c |
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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" " | |
| 5 #for $i, $input in enumerate($inputs) | |
| 6 ${input.in_file} | |
| 7 #end for | |
| 8 " | |
| 9 " | |
| 10 #for $i, $input in enumerate($inputs) | |
| 11 ${input.id} | |
| 12 #end for | |
| 13 " | |
| 14 $reference $out_file "$selection" "$out_table" | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <repeat name="inputs" title="inputs" min="1" default="1"> | |
| 18 <param name="in_file" type="data" label="Input excel or IMGT zip file" /> | |
| 19 <param name="id" type="text" label="ID (alpha-numeric, no spaces)" /> | |
| 20 </repeat> | |
| 21 <param name="reference" type="data" format="fasta" label="Reference fasta file" /> | |
| 22 <param name="ss" type="select" label="Selection Statistic"> | |
| 23 <option value="1">Focused</option> | |
| 24 <option value="2">Local</option> | |
| 25 </param> | |
| 26 <param name="species" type="select" label="SHM Targeting Model"> | |
| 27 <option value="1">Human</option> | |
| 28 <option value="2">Mouse</option> | |
| 29 </param> | |
| 30 <param name="substitution" type="select" label="Substitution Model"> | |
| 31 <option value="1">Smith DS et al. 1996</option> | |
| 32 <option value="0">Uniform substitution</option> | |
| 33 <option value="5">FiveS</option> | |
| 34 </param> | |
| 35 <param name="mutability" type="select" label="Mutability Model"> | |
| 36 <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option> | |
| 37 <option value="0">Uniform mutability</option> | |
| 38 <option value="5">FiveS</option> | |
| 39 </param> | |
| 40 <param name="clonal" type="select" label="Sequences are clonal"> | |
| 41 <option value="0">Independent sequences</option> | |
| 42 <option value="1">Clonally related</option> | |
| 43 <option value="2">Clonally related and only non-terminal mutations</option> | |
| 44 </param> | |
| 45 <param name="fixindels" type="select" label="Fix Indels"> | |
| 46 <option value="0">Do Nothing</option> | |
| 47 <option value="1">Try and fix Indels</option> | |
| 48 </param> | |
| 49 <param name="boundaries" type="text" value="25:26:38:55:65:104:-" size="40" label="Custom Boundaries (FWR1Start:FWR1End:CDR1End:FWR2End:CDR3End:FWR3End:CDR3End)" /> | |
| 50 <param name="selection" type="select" label="Unique Selection Definition"> | |
| 51 <option value="VGene,AA.JUNCTION">VGene, AA CDR3</option> | |
| 52 <option value="VGene,JGene,AA.JUNCTION">VGene, JGene, AA CDR3</option> | |
| 53 <option value="VGene,DGene,JGene,AA.JUNCTION">VGene, DGene, JGene, AA CDR3</option> | |
| 54 <option value="Sequence.ID">None</option> | |
| 55 </param> | |
| 56 </inputs> | |
| 57 <outputs> | |
| 58 <data format="pdf" name="out_file" label = "Baseline PDF on ${on_string}"/> | |
| 59 <data format="tabular" name="out_table" label = "Baseline Table on ${on_string}"/> | |
| 60 </outputs> | |
| 61 <help> | |
| 62 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27. | |
| 63 | |
| 64 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. | |
| 65 | |
| 66 **Boundaries** | |
| 67 | |
| 68 IMGT® No CDR3: "1:26:38:55:65:104:-" | |
| 69 | |
| 70 IMGT®: "1:26:38:55:65:104:116" | |
| 71 | |
| 72 </help> | |
| 73 </tool> |