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1 <tool id="polyphen2_web" name="PolyPhen-2 Webservice">
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2 <description>Compute functional impact of SNVs </description>
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3 <requirements>
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4 <requirement type="package" version="4.1.0">beautifulsoup4</requirement>
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5 <requirement type="python-module">bs4</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 polyphen2_web.py --ucscdb $ucscdb
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9 --model $model
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10 --filter $filter
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11 --function $function
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12 --input $input
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13 --log $log_file
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14 --full $full_file
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15 --short $short_file
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16 --snp $snp_file
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17 </command>
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18 <inputs>
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19 <param format="txt" name="input" type="data" label="Variants File" />
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20 <param name="ucscdb" type="select" label="Genome Assembly">
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21 <option value="hg19">GRCh37/hg19</option>
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22 <option value="hg18">NCBI36/hg18</option>
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23 </param>
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24 <param name="model" type="select" label="Classifier Model">
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25 <option value="HumDiv">HumDiv</option>
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26 <option value="HumVar">HumVar</option>
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27 </param>
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28 <param name="filter" type="select" label="Transcripts">
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29 <option value="All">All</option>
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30 <option value="Canonical">Canonical</option>
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31 <option value="CCDS">CCDS</option>
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32 </param>
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33 <param name="function" type="select" label="Annotations">
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34 <option value="c">Canonical</option>
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35 <option value="m">CCDS</option>
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36 <option value="All">All</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="log_file" label="${tool.name} on ${on_string}: log" />
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41 <data format="tabular" name="full_file" label="${tool.name} on ${on_string}: full"/>
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42 <data format="tabular" name="short_file" label="${tool.name} on ${on_string}: short"/>
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43 <data format="tabular" name="snp_file" label="${tool.name} on ${on_string}: snp"/>
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="input" value="polyphen2_input.txt"/>
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49 <param name="ucscdb" value="hg19"/>
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50 <param name="model" value="HumDiv"/>
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51 <param name="filter" value="All"/>
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52 <param name="function" value="All"/>
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53 <output name="log_file" file="polyphen2_log.txt"/>
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54 <output name="full_file" file="polyphen2_full.txt"/>
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55 <output name="short_file" file="polyphen2_short.txt"/>
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56 <output name="snp_file" file="polyphen2_snp.txt"/>
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57 </test>
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58 </tests>
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59 <help>
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60 **What it does**
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61 This tool interacts with the Web Version of Polyphen2 hosted at http://genetics.bwh.harvard.edu/pph2/
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62
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63 PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions
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64 on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
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65
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66 .. class:: infomark
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67
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68 * HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions
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69
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70 .. class:: infomark
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71
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72 * HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions
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73
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74 .. class:: infomark
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75
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76
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77 '''Input format''':
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78
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79
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80 chr22:30421786 A/T
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81
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82 chr22:29446079 A/G
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83
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84 chr22:40814500 A/G
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85
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86 chr22:40815256 C/T
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87
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88
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89 **Citations**
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90
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91 If you use this tool please cite:
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92
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93 Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).
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94 "A method and server for predicting damaging missense mutations."
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95
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96 </help>
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97 </tool>
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98
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99
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100
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101
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102
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103
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