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comparison polyphen2_web/polyphen2_web.xml @ 0:b319f980c9e6 draft

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author saketkc
date Mon, 14 Apr 2014 17:27:06 -0400
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1 <tool id="polyphen2_web" name="PolyPhen-2 Webservice">
2 <description>Compute functional impact of SNVs </description>
3 <requirements>
4 <requirement type="package" version="4.1.0">beautifulsoup4</requirement>
5 <requirement type="python-module">bs4</requirement>
6 </requirements>
7 <command interpreter="python">
8 polyphen2_web.py --ucscdb $ucscdb
9 --model $model
10 --filter $filter
11 --function $function
12 --input $input
13 --log $log_file
14 --full $full_file
15 --short $short_file
16 --snp $snp_file
17 </command>
18 <inputs>
19 <param format="txt" name="input" type="data" label="Variants File" />
20 <param name="ucscdb" type="select" label="Genome Assembly">
21 <option value="hg19">GRCh37/hg19</option>
22 <option value="hg18">NCBI36/hg18</option>
23 </param>
24 <param name="model" type="select" label="Classifier Model">
25 <option value="HumDiv">HumDiv</option>
26 <option value="HumVar">HumVar</option>
27 </param>
28 <param name="filter" type="select" label="Transcripts">
29 <option value="All">All</option>
30 <option value="Canonical">Canonical</option>
31 <option value="CCDS">CCDS</option>
32 </param>
33 <param name="function" type="select" label="Annotations">
34 <option value="c">Canonical</option>
35 <option value="m">CCDS</option>
36 <option value="All">All</option>
37 </param>
38 </inputs>
39 <outputs>
40 <data format="tabular" name="log_file" label="${tool.name} on ${on_string}: log" />
41 <data format="tabular" name="full_file" label="${tool.name} on ${on_string}: full"/>
42 <data format="tabular" name="short_file" label="${tool.name} on ${on_string}: short"/>
43 <data format="tabular" name="snp_file" label="${tool.name} on ${on_string}: snp"/>
44 </outputs>
45
46 <tests>
47 <test>
48 <param name="input" value="polyphen2_input.txt"/>
49 <param name="ucscdb" value="hg19"/>
50 <param name="model" value="HumDiv"/>
51 <param name="filter" value="All"/>
52 <param name="function" value="All"/>
53 <output name="log_file" file="polyphen2_log.txt"/>
54 <output name="full_file" file="polyphen2_full.txt"/>
55 <output name="short_file" file="polyphen2_short.txt"/>
56 <output name="snp_file" file="polyphen2_snp.txt"/>
57 </test>
58 </tests>
59 <help>
60 **What it does**
61 This tool interacts with the Web Version of Polyphen2 hosted at http://genetics.bwh.harvard.edu/pph2/
62
63 PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions
64 on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
65
66 .. class:: infomark
67
68 * HumDiv model uses 5% / 10% FPR thresholds for “probably damaging” / “possibly damaging” predictions
69
70 .. class:: infomark
71
72 * HumVar model uses 10% / 20% FPR thresholds for “probably damaging” / “possibly damaging” predictions
73
74 .. class:: infomark
75
76
77 '''Input format''':
78
79
80 chr22:30421786 A/T
81
82 chr22:29446079 A/G
83
84 chr22:40814500 A/G
85
86 chr22:40815256 C/T
87
88
89 **Citations**
90
91 If you use this tool please cite:
92
93 Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).
94 "A method and server for predicting damaging missense mutations."
95
96 </help>
97 </tool>
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