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1 <tool id="mutationassesor_web" name="MutationAssesor">
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2 <description>MutationAssesor 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 </requirements>
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7 <command interpreter="python">mutation_assesor.py --input $input --output $output
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8 #if $options.protein == "yes"
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9 --protein
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10 #else
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11 $options.hg19
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12 #end if
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13 </command>
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14 <inputs>
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15 <param name="input" format="txt" type="data" label="Input variants" />
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16 <conditional name="options">
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17 <param name="protein" type="select" label="Protein Input">
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18 <option value="yes">Yes</option>
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19 <option value="no">No</option>
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20 </param>
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21 <when value="no">
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22 <param name="hg19" type="select" label="hg19">
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23 <option value="--hg19">Yes</option>
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24 <option value="">No</option>
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25 </param>
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26 </when>
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27 </conditional>
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28 </inputs>
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29 <outputs>
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30 <data name="output" format="csv"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" value="ma_proper_nucleotide.csv"/>
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35 <param name="hg19" value="--hg19"/>
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36 <param name="protein" value="no"/>
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37 <output name="output" file="ma_nucleotide_output.csv"/>
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38 </test>
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39 <test>
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40 <param name="input" value="ma_proper_protein.csv"/>
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41 <param name="protein" value="yes"/>
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42 <output name="output" file="ma_protein_output.csv"/>
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43 </test>
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44 <test>
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45 <param name="input" value="mutationassessor_input.txt"/>
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46 <param name="protein" value="yes"/>
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47 <output name="output" file="mutationassessor_output.tsv" lines_diff="2"/>
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48 </test>
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49 </tests>
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50 <help>
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51
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52
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53 **What it does**
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54
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55 This script calls MutationAssesor(http://mutationassessor.org/) Web API to fetch
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56 Mutation Assesor scores and associated output.
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57
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58 Input is a tab separated or comma separated varaibles file. MutationAssesor
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59 server accepts list of variants, one variant per line, plus optional text thrown in
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60 which might be a description of the variants in genomic coordinates. The
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61 variants are assumed to be coming from '+' strand:
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62 <genome build>,<chromosome>,<position>,<reference allele>,<substituted allele>
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63
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64
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65 Genome build is optional. By default 'hg18' build is used.
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66 Input needs to be formatted in the following format:
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67
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68 1. Nucleotide space:
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69
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70 13,32912555,G,T BRCA2
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71
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72 7,55178574,G,A GBM
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73
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74 7,55178574,G,A GBM
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75
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76 Note that the tool takes care of prepending 'hg19' while running the tool, if you
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77 select 'yes' under 'hg19' label
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78
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79 2. Protein Space
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80 <protein ID> <variant> <text>, where <protein ID> can be :
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81
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82 1. Uniprot protein accession (i.e. EGFR_HUMAN)
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83 2. NCBI Refseq protein ID (i.e. NP_005219)
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84
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85 EGFR_HUMAN R521K
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86 EGFR_HUMAN R98Q Polymorphism
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87 EGFR_HUMAN G719D disease
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88 NP_000537 G356A
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89 NP_000537 G360A dbSNP:rs35993958
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90 NP_000537 S46A Abolishes phosphorylation
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91
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92
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93
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94 **Citations**
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95
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96 If you use this tool in Galaxy, please cite :
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97 Reva B, Antipin Y, Sander C. Nucleic Acids Research (2011)
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98 "Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics"
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99
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100 Reva, B.A., Antipin, Y.A. and Sander, C. (2007) Genome Biol, 8, R232.
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101 "Determinants of protein function revealed by combinatorial entropy optimization"
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102
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103
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104
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105 </help>
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106 </tool>
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107
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