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author | saket-choudhary |
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date | Tue, 07 Oct 2014 19:40:29 -0400 |
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<tool id="mutationassesor_web" name="MutationAssesor"> <description>MutationAssesor web service</description> <requirements> <requirement type="package" version="2.2.1">requests</requirement> <requirement type="python-module">requests</requirement> </requirements> <command interpreter="python">mutation_assesor.py --input $input --output $output #if $options.protein == "yes" --protein #else $options.hg19 #end if </command> <inputs> <param name="input" format="txt" type="data" label="Input variants" /> <conditional name="options"> <param name="protein" type="select" label="Protein Input"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="no"> <param name="hg19" type="select" label="hg19"> <option value="--hg19">Yes</option> <option value="">No</option> </param> </when> </conditional> </inputs> <outputs> <data name="output" format="csv"/> </outputs> <tests> <test> <param name="input" value="ma_proper_nucleotide.csv"/> <param name="hg19" value="--hg19"/> <param name="protein" value="no"/> <output name="output" file="ma_nucleotide_output.csv"/> </test> <test> <param name="input" value="ma_proper_protein.csv"/> <param name="protein" value="yes"/> <output name="output" file="ma_protein_output.csv"/> </test> <test> <param name="input" value="mutationassessor_input.txt"/> <param name="protein" value="yes"/> <output name="output" file="mutationassessor_output.tsv" lines_diff="2"/> </test> </tests> <help> **What it does** This script calls MutationAssesor(http://mutationassessor.org/) Web API to fetch Mutation Assesor scores and associated output. Input is a tab separated or comma separated varaibles file. MutationAssesor server accepts list of variants, one variant per line, plus optional text thrown in which might be a description of the variants in genomic coordinates. The variants are assumed to be coming from '+' strand: <genome build>,<chromosome>,<position>,<reference allele>,<substituted allele> Genome build is optional. By default 'hg18' build is used. Input needs to be formatted in the following format: 1. Nucleotide space: 13,32912555,G,T BRCA2 7,55178574,G,A GBM 7,55178574,G,A GBM Note that the tool takes care of prepending 'hg19' while running the tool, if you select 'yes' under 'hg19' label 2. Protein Space <protein ID> <variant> <text>, where <protein ID> can be : 1. Uniprot protein accession (i.e. EGFR_HUMAN) 2. NCBI Refseq protein ID (i.e. NP_005219) EGFR_HUMAN R521K EGFR_HUMAN R98Q Polymorphism EGFR_HUMAN G719D disease NP_000537 G356A NP_000537 G360A dbSNP:rs35993958 NP_000537 S46A Abolishes phosphorylation **Citations** If you use this tool in Galaxy, please cite : Reva B, Antipin Y, Sander C. Nucleic Acids Research (2011) "Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics" Reva, B.A., Antipin, Y.A. and Sander, C. (2007) Genome Biol, 8, R232. "Determinants of protein function revealed by combinatorial entropy optimization" </help> </tool>