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1 <tool id="snpEff" name="SnpEff" version="3.1">
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2 <description>Variant effect and annotation</description>
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3 <!--
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4 You will need to change the path to wherever your installation is.
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5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
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7 -->
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8 <requirements>
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9 <requirement type="package" version="3.1">snpEff</requirement>
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10 </requirements>
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11 <command>
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12 export SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
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13 if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
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14 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
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15 fi;
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16 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
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17 <inputs>
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18 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
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19
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20 <param name="inputFormat" type="select" label="Input format">
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21 <option value="vcf">VCF</option>
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22 <option value="txt">Tabular</option>
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23 <option value="pileup">Pileup</option>
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24 <option value="bed">BED</option>
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25 </param>
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26
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27 <param name="outputFormat" type="select" label="Output format">
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28 <option value="txt">Tabular</option>
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29 <option value="vcf">VCF (only if input is VCF)</option>
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30 <option value="bed">BED</option>
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31 <option value="bedAnn">BED Annotations</option>
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32 </param>
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33
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34 <param name="genomeVersion" type="select" label="Genome">
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35 <options from_file="snpeffect_genomedb.loc">
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36 <column name="name" index="1"/>
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37 <column name="value" index="0"/>
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38 </options>
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39 </param>
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40
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41 <param name="udLength" type="select" label="Upstream / Downstream length">
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42 <option value="0">No upstream / downstream intervals (0 bases)</option>
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43 <option value="200">200 bases</option>
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44 <option value="500">500 bases</option>
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45 <option value="1000">1000 bases</option>
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46 <option value="2000">2000 bases</option>
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47 <option value="5000" selected="true">5000 bases</option>
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48 <option value="10000">10000 bases</option>
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49 <option value="20000">20000 bases</option>
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50 </param>
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51
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52 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
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53 <option value="">No filter (analyze everything)</option>
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54 <option value="-hom">Analyze homozygous sequence changes only </option>
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55 <option value="-het">Analyze heterozygous sequence changes only </option>
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56 </param>
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57
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58 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
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59 <option value="">No filter (analyze everything)</option>
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60 <option value="-del">Analyze deletions only </option>
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61 <option value="-ins">Analyze insertions only </option>
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62 <option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option>
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63 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
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64 </param>
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65
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66 <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output">
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67 <option value="None" selected="true">None</option>
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68 <option value="downstream">Do not show DOWNSTREAM changes </option>
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69 <option value="intergenic">Do not show INTERGENIC changes </option>
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70 <option value="intron">Do not show INTRON changes </option>
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71 <option value="upstream">Do not show UPSTREAM changes </option>
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72 <option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
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73 </param>
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74
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75 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
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76 <option value="">Use default (based on input type)</option>
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77 <option value="-0">Force zero-based positions (both input and output)</option>
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78 <option value="-1">Force one-based positions (both input and output)</option>
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79 </param>
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80 </inputs>
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81 <outputs>
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82 <data format="tabular" name="output" >
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83 <change_format>
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84 <when input="outputFormat" value="txt" format="tabular" />
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85 <when input="outputFormat" value="vcf" format="vcf" />
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86 <when input="outputFormat" value="bed" format="bed" />
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87 <when input="outputFormat" value="bedAnn" format="bed" />
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88 </change_format>
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89 </data>
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90 <data format="html" name="statsFile" />
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91 </outputs>
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92 <stdio>
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93 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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94 <exit_code range="1:" level="fatal" description="Error" />
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95 </stdio>
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96 <help>
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97
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98 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
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99
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100 For details about this tool, please go to http://snpEff.sourceforge.net
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101
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102 </help>
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103 </tool>
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104
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