|
0
|
1 <tool id="variant_effect_predictor" name="Variant Effect Predictor" version="2.6">
|
|
|
2 <description>Get consequences of variants</description>
|
|
|
3 <command interpreter="perl">
|
|
|
4 variant_effect_predictor.pl
|
|
|
5 -format vcf -quiet -force -fork 4
|
|
|
6 -cache -dir /mnt/galaxyIndices/vep/
|
|
|
7 -i $input -o $output $output_format
|
|
|
8 $check_existing $check_ref $regulatory
|
|
|
9 $hgnc
|
|
|
10 -terms $terms $sift $polyphen
|
|
|
11 </command>
|
|
|
12 <inputs>
|
|
|
13 <param format="vcf" name="input" type="data" label="Input file"/>
|
|
|
14
|
|
|
15 <param name="output_format" type="select" label="Output format">
|
|
|
16 <option value="" selected="true">Default</option>
|
|
|
17 <option value="-vcf">VCF</option>
|
|
|
18 <option value="-gvf">GVF</option>
|
|
|
19 </param>
|
|
|
20
|
|
|
21 <param name="terms" type="select" label="Consequence types">
|
|
|
22 <option value="so" selected="true">Sequence Ontology (SO)</option>
|
|
|
23 <option value="ensembl">Ensembl</option>
|
|
|
24 </param>
|
|
|
25
|
|
|
26 <param name="sift" type="select" label="SIFT predictions">
|
|
|
27 <option value="">None</option>
|
|
|
28 <option value="-sift s">Score only</option>
|
|
|
29 <option value="-sift p">Prediction only</option>
|
|
|
30 <option value="-sift b" selected="true">Score and prediction</option>
|
|
|
31 </param>
|
|
|
32
|
|
|
33 <param name="polyphen" type="select" label="PolyPhen predictions">
|
|
|
34 <option value="">None</option>
|
|
|
35 <option value="-polyphen s">Score only</option>
|
|
|
36 <option value="-polyphen p">Prediction only</option>
|
|
|
37 <option value="-polyphen b" selected="true">Score and prediction</option>
|
|
|
38 </param>
|
|
|
39
|
|
|
40
|
|
|
41 <param name="check_existing" type="select" label="Check for existing co-located variations">
|
|
|
42 <option value="">no</option>
|
|
|
43 <option value="-check_existing" selected="true">yes</option>
|
|
|
44 </param>
|
|
|
45
|
|
|
46 <param name="check_ref" type="select" label="Sanity check supplied reference allele against Ensembl reference">
|
|
|
47 <option value="" selected="true">no</option>
|
|
|
48 <option value="-check_ref">yes</option>
|
|
|
49 </param>
|
|
|
50
|
|
|
51 <param name="regulatory" type="select" label="Get regulatory consequences">
|
|
|
52 <option value="">no</option>
|
|
|
53 <option value="-regulatory" selected="true">yes</option>
|
|
|
54 </param>
|
|
|
55
|
|
|
56 <param name="hgnc" type="select" label="Add HGNC identifiers for genes where available">
|
|
|
57 <option value="" selected="true">no</option>
|
|
|
58 <option value="-hgnc">yes</option>
|
|
|
59 </param>
|
|
|
60
|
|
|
61 </inputs>
|
|
|
62 <outputs>
|
|
|
63 <data format="tabular" name="output" />
|
|
|
64 </outputs>
|
|
|
65
|
|
|
66 <help>
|
|
|
67 This tool calculates consequences of variants using Ensembl annotations
|
|
|
68 </help>
|
|
|
69
|
|
|
70 </tool> |
