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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" $in_file $out_file.files_path result $out_file $out_file2
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5 </command>
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6 <inputs>
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7 <param name="in_file" format="fasta" type="data" label="Data to Process" />
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8 <param name="ss" type="select" label="Selection Statistic">
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9 <option value="1">Focused</option>
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10 <option value="2">Local</option>
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11 </param>
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12 <param name="species" type="select" label="SHM Targeting Model">
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13 <option value="1">Human</option>
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14 <option value="2">Mouse</option>
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15 </param>
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16 <param name="substitution" type="select" label="Substitution Model">
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17 <option value="0">Uniform substitution</option>
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18 <option value="1">Smith DS et al. 1996</option>
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19 <option value="5">FiveS</option>
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20 </param>
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21 <param name="mutability" type="select" label="Mutability Model">
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22 <option value="0">Uniform mutability</option>
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23 <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
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24 <option value="5">FiveS</option>
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25 </param>
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26 <param name="clonal" type="select" label="Sequences are clonal">
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27 <option value="0">Independent sequences</option>
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28 <option value="1">Clonally related</option>
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29 <option value="2">Clonally related and only non-terminal mutations</option>
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30 </param>
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31 <param name="fixindels" type="select" label="Fix Indels">
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32 <option value="0">Do Nothing</option>
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33 <option value="1">Try and fix Indels</option>
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34 </param>
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35 <param name="boundaries" type="select" label="FWR/CDR3 Boundaries">
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36 <option value="1:26:38:55:65:104:116">IMGT®</option>
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37 <option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data format="tabular" name="out_file" label = "${tool.name} on ${on_string}: result"/>
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42 <data format="data" name="out_file2" label = "${tool.name} on ${on_string}: RData"/>
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43 </outputs>
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44 <help>
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45 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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46
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47 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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48
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49 </help>
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50 </tool>
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