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comparison baseline.xml @ 2:94fada165724 draft

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author davidvanzessen
date Wed, 13 Aug 2014 07:32:38 -0400
parents d685e7ba0ed4
children 38c038c17d0c
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1:e8dd8474aecb 2:94fada165724
1 <tool id="baseline_bayesian_estimation" name="Baseline" version="1.0"> 1 <tool id="baseline_bayesian_estimation" name="Baseline" version="1.0">
2 <description>Bayesian Estimation of Antigen-Driven Selection</description> 2 <description>Bayesian Estimation of Antigen-Driven Selection</description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 wrapper.sh $ss $species $substitution $mutability $clonal $fixindels "$boundaries" $in_file $out_file.files_path result $out_file $out_file2 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
5 </command> 15 </command>
6 <inputs> 16 <inputs>
7 <param name="in_file" format="fasta" type="data" label="Data to Process" /> 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" />
8 <param name="ss" type="select" label="Selection Statistic"> 22 <param name="ss" type="select" label="Selection Statistic">
9 <option value="1">Focused</option> 23 <option value="1">Focused</option>
10 <option value="2">Local</option> 24 <option value="2">Local</option>
11 </param> 25 </param>
12 <param name="species" type="select" label="SHM Targeting Model"> 26 <param name="species" type="select" label="SHM Targeting Model">
13 <option value="1">Human</option> 27 <option value="1">Human</option>
14 <option value="2">Mouse</option> 28 <option value="2">Mouse</option>
15 </param> 29 </param>
16 <param name="substitution" type="select" label="Substitution Model"> 30 <param name="substitution" type="select" label="Substitution Model">
31 <option value="1">Smith DS et al. 1996</option>
17 <option value="0">Uniform substitution</option> 32 <option value="0">Uniform substitution</option>
18 <option value="1">Smith DS et al. 1996</option>
19 <option value="5">FiveS</option> 33 <option value="5">FiveS</option>
20 </param> 34 </param>
21 <param name="mutability" type="select" label="Mutability Model"> 35 <param name="mutability" type="select" label="Mutability Model">
36 <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
22 <option value="0">Uniform mutability</option> 37 <option value="0">Uniform mutability</option>
23 <option value="1">Tri-nucleotide (Shapiro GS et al. 2002)</option>
24 <option value="5">FiveS</option> 38 <option value="5">FiveS</option>
25 </param> 39 </param>
26 <param name="clonal" type="select" label="Sequences are clonal"> 40 <param name="clonal" type="select" label="Sequences are clonal">
27 <option value="0">Independent sequences</option> 41 <option value="0">Independent sequences</option>
28 <option value="1">Clonally related</option> 42 <option value="1">Clonally related</option>
31 <param name="fixindels" type="select" label="Fix Indels"> 45 <param name="fixindels" type="select" label="Fix Indels">
32 <option value="0">Do Nothing</option> 46 <option value="0">Do Nothing</option>
33 <option value="1">Try and fix Indels</option> 47 <option value="1">Try and fix Indels</option>
34 </param> 48 </param>
35 <param name="boundaries" type="select" label="FWR/CDR3 Boundaries"> 49 <param name="boundaries" type="select" label="FWR/CDR3 Boundaries">
50 <option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
36 <option value="1:26:38:55:65:104:116">IMGT®</option> 51 <option value="1:26:38:55:65:104:116">IMGT®</option>
37 <option value="1:26:38:55:65:104:-">IMGT® No CDR3</option>
38 </param> 52 </param>
39 </inputs> 53 </inputs>
40 <outputs> 54 <outputs>
41 <data format="tabular" name="out_file" label = "${tool.name} on ${on_string}: result"/> 55 <data format="pdf" name="out_file" label = "Baseline on ${on_string}"/>
42 <data format="data" name="out_file2" label = "${tool.name} on ${on_string}: RData"/>
43 </outputs> 56 </outputs>
44 <help> 57 <help>
45 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27. 58 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.
46 59
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. 60 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.