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1 <tool id="baseline_bayesian_estimation" name="Baseline" version="1.0">
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2 <description>Bayesian Estimation of Antigen-Driven Selection</description>
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3 <command interpreter="bash">
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4 wrapper.sh $ss $species $substitution $mutability $clonal $fixindels "$boundaries" "
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5 #for $i, $input in enumerate($inputs)
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6 ${input.in_file}
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7 #end for
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8 "
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9 "
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10 #for $i, $input in enumerate($inputs)
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11 ${input.id}
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12 #end for
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13 "
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14 $reference $out_file "$selection" "$out_table"
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15 </command>
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16 <inputs>
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17 <repeat name="inputs" title="inputs" min="1" default="1">
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18 <param name="in_file" type="data" label="Input excel or IMGT zip file" />
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19 <param name="id" type="text" label="ID (alpha-numeric, no spaces)" />
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20 </repeat>
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21 <param name="reference" type="data" format="fasta" label="Reference fasta file" />
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22 <param name="ss" type="select" label="Selection Statistic">
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23 <option value="1">Focused</option>
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24 <option value="2">Local</option>
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25 </param>
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26 <param name="species" type="select" label="SHM Targeting Model">
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27 <option value="1">Human</option>
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28 <option value="2">Mouse</option>
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29 </param>
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30 <param name="substitution" type="select" label="Substitution Model">
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31 <option value="1">Smith DS et al. 1996</option>
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32 <option value="0">Uniform substitution</option>
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33 <option value="5">FiveS</option>
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34 </param>
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35 <param name="mutability" type="select" label="Mutability Model">
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36 <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
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37 <option value="0">Uniform mutability</option>
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38 <option value="5">FiveS</option>
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39 </param>
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40 <param name="clonal" type="select" label="Sequences are clonal">
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41 <option value="0">Independent sequences</option>
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42 <option value="1">Clonally related</option>
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43 <option value="2">Clonally related and only non-terminal mutations</option>
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44 </param>
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45 <param name="fixindels" type="select" label="Fix Indels">
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46 <option value="0">Do Nothing</option>
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47 <option value="1">Try and fix Indels</option>
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48 </param>
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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)" />
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50 <param name="selection" type="select" label="Unique Selection Definition">
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51 <option value="VGene,AA.JUNCTION">VGene, AA CDR3</option>
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52 <option value="VGene,JGene,AA.JUNCTION">VGene, JGene, AA CDR3</option>
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53 <option value="VGene,DGene,JGene,AA.JUNCTION">VGene, DGene, JGene, AA CDR3</option>
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54 <option value="Sequence.ID">None</option>
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55 </param>
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56 </inputs>
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57 <outputs>
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58 <data format="pdf" name="out_file" label = "Baseline PDF on ${on_string}"/>
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59 <data format="tabular" name="out_table" label = "Baseline Table on ${on_string}"/>
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60 </outputs>
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61 <help>
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62 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.
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63
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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.
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65
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66 **Boundaries**
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67
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68 IMGT® No CDR3: "1:26:38:55:65:104:-"
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69
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70 IMGT®: "1:26:38:55:65:104:116"
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71
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72 </help>
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73 </tool>
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