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1 <tool id="vep_rest" name="VEP Rest">
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2 <description>VEP Web Service</description>
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3 <requirements>
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4 <requirement type="package" version="2.2.1">requests</requirement>
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5 <requirement type="python-module">requests</requirement>
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6 <requirement type="package" version="2.2.1">pyvcf</requirement>
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7 <requirement type="python-module">pyvcf</requirement>
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8 </requirements>
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9 <command interpreter="python">
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10 vep_rest.py --input_file $input --output_file $output
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11 </command>
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12 <inputs>
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13 <param name="input" format="vcf" type="data" label="Input variants" />
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14 </inputs>
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15 <outputs>
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16 <data name="output" format="txt"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input" value="vep_input.vcf"/>
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21 <output name="output" file="vep_output.txt"/>
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22 </test>
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23 </tests>
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24 <help>
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25
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26
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27 **What it does**
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28
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29 This script calls VEP Rest webserice for GRCh37(http://grch37.rest.ensembl.org/) to fetch
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30 consequences of variations in the proteins ONLY. Variations in transcripts are IGNORED.
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31
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32 Input is a VCF file.[http://samtools.github.io/hts-specs/VCFv4.2.pdf]
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33
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34 Output is a text file with each line beginning with Protein identifier followed by comma separated substituions.
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35 Example:
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36
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37 ENSP00000393181, S52C,G66W,P77S,R85K,V92M,L107I
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38 ENSP00000471152, G45R,R42T,A40T,G19E,L11F,T3M
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39 ENSP00000411579, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R
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40 ENSP00000349216, R9K,V16M,L31I,E48A,E61K,R77H,R80P,E94K,S95L,P96R
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41 ENSP00000342313, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R
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42
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43
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44 **Citations**
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45
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46 If you use this tool in Galaxy, please cite :
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47 McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
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48 Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
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49 Bioinformatics 26(16):2069-70(2010)
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50 doi:10.1093/bioinformatics/btq330
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51
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52
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53 </help>
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54 </tool>
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55
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