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1 <tool id="snpEff" name="SnpEff" version="3.3">
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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 Options:
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8 -a , -around : Show N codons and amino acids around change (only in coding regions). Default is 0 codons.
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9 -i <format> : Input format [ vcf, txt, pileup, bed ]. Default: VCF.
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10 -o <format> : Ouput format [ txt, vcf, gatk, bed, bedAnn ]. Default: VCF.
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11 -interval : Use a custom interval file (you may use this option many times)
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12 -chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
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13 -s, -stats : Name of stats file (summary). Default is 'snpEff_summary.html'
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14 -t : Use multiple threads (implies '-noStats'). Default 'off'
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15
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16 Sequence change filter options:
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17 -del : Analyze deletions only
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18 -ins : Analyze insertions only
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19 -hom : Analyze homozygous variants only
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20 -het : Analyze heterozygous variants only
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21 -minQ X, -minQuality X : Filter out variants with quality lower than X
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22 -maxQ X, -maxQuality X : Filter out variants with quality higher than X
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23 -minC X, -minCoverage X : Filter out variants with coverage lower than X
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24 -maxC X, -maxCoverage X : Filter out variants with coverage higher than X
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25 -nmp : Only MNPs (multiple nucleotide polymorphisms)
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26 -snp : Only SNPs (single nucleotide polymorphisms)
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27
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28 Results filter options:
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29 -fi <bedFile> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
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30 -no-downstream : Do not show DOWNSTREAM changes
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31 -no-intergenic : Do not show INTERGENIC changes
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32 -no-intron : Do not show INTRON changes
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33 -no-upstream : Do not show UPSTREAM changes
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34 -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
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35
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36 Annotations options:
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37 -cancer : Perform 'cancer' comparissons (Somatic vs Germline). Default: false
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38 -canon : Only use canonical transcripts.
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39 -geneId : Use gene ID instead of gene name (VCF output). Default: false
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40 -hgvs : Use HGVS annotations for amino acid sub-field. Default: false
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41 -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
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42 -reg <name> : Regulation track to use (this option can be used add several times).
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43 -oicr : Add OICR tag in VCF file. Default: false
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44 -onlyReg : Only use regulation tracks.
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45 -onlyTr <file.txt> : Only use the transcripts in this file. Format: One transcript ID per line.
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46 -sequenceOntolgy : Use Sequence Ontolgy terms. Default: false
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47 -ss, -spliceSiteSize <int> : Set size for splice sites (donor and acceptor) in bases. Default: 2
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48 -ud, -upDownStreamLen <int> : Set upstream downstream interval length (in bases)
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49
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50 Generic options:
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51 -0 : File positions are zero-based (same as '-inOffset 0 -outOffset 0')
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52 -1 : File positions are one-based (same as '-inOffset 1 -outOffset 1')
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53 -c , -config : Specify config file
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54 -h , -help : Show this help and exit
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55 -if, -inOffset : Offset input by a number of bases. E.g. '-inOffset 1' for one-based input files
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56 -of, -outOffset : Offset output by a number of bases. E.g. '-outOffset 1' for one-based output files
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57 -noLog : Do not report usage statistics to server
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58 -noStats : Do not create stats (summary) file
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59 -q , -quiet : Quiet mode (do not show any messages or errors)
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60 -v , -verbose : Verbose mode
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61
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62 -->
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63 <requirements>
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64 <requirement type="package" version="3.3">snpEff</requirement>
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65 </requirements>
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66 <command>
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3
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67 #if str( $intervals ) != 'None':
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68 ln -s $intervals tempIntervals.bed &&
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2
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69 #end if
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1
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70 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
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71 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
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72 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
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73 fi";
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74 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength
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75 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
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76 -spliceSiteSize $spliceSiteSize
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77 #end if
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78 #if $filterIn and $filterIn.__str__ != 'no_filter':
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79 -$filterIn
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80 #end if
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81 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
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82 -$filterHomHet
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83 #end if
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84 #if $annotations and $annotations.__str__ != '':
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85 -#slurp
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86 #echo ' -'.join($annotations.__str__.split(','))
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87 #end if
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88 #if $filterOut and $filterOut.__str__ != '':
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89 -#slurp
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90 #echo ' -'.join($filterOut.__str__.split(','))
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91 #end if
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92 #if str( $transcripts ) != 'None':
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93 -onlyTr $transcripts
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94 #end if
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95 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
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96 -interval tempIntervals.bed
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97 #end if
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98 #if $statsFile:
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99 -stats $statsFile
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100 #end if
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101 #if $offset.__str__ != '':
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102 -${offset}
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103 #end if
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104 #if $chr.__str__.strip() != '':
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105 -chr "$chr"
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106 #end if
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107 $noLog $genomeVersion $input > $snpeff_output
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108 </command>
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109 <inputs>
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110 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
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111
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112 <param name="inputFormat" type="select" label="Input format">
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113 <option value="vcf" selected="true">VCF</option>
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114 <option value="txt">Tabular (Deprecated)</option>
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115 <option value="pileup">Pileup (Deprecated)</option>
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116 <option value="bed">BED (Deprecated)</option>
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117 </param>
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118
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119 <param name="outputFormat" type="select" label="Output format">
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120 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
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121 <option value="txt">Tabular</option>
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122 <option value="bed">BED</option>
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123 <option value="bedAnn">BED Annotations</option>
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124 </param>
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125
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126 <param name="genomeVersion" type="select" label="Genome">
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127 <!--GENOME DESCRIPTION-->
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128 <options from_file="snpeffect_genomedb.loc">
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129 <column name="name" index="1"/>
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130 <column name="value" index="0"/>
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131 </options>
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132 </param>
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133
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134 <param name="udLength" type="select" label="Upstream / Downstream length">
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135 <option value="0">No upstream / downstream intervals (0 bases)</option>
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136 <option value="200">200 bases</option>
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137 <option value="500">500 bases</option>
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138 <option value="1000">1000 bases</option>
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139 <option value="2000">2000 bases</option>
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140 <option value="5000" selected="true">5000 bases</option>
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141 <option value="10000">10000 bases</option>
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142 <option value="20000">20000 bases</option>
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143 </param>
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144
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145 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2">
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146 <option value="1">1 base</option>
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147 <option value="2">2 bases</option>
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148 <option value="3">3 bases</option>
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149 <option value="4">4 bases</option>
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150 <option value="5">5 bases</option>
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151 <option value="6">6 bases</option>
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152 <option value="7">7 bases</option>
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153 <option value="8">8 bases</option>
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154 <option value="9">9 bases</option>
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155 </param>
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156
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157 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
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158 <option value="no_filter" selected="true">No filter (analyze everything)</option>
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159 <option value="hom">Analyze homozygous sequence changes only </option>
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160 <option value="het">Analyze heterozygous sequence changes only </option>
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161 </param>
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162
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163 <!-- The tool testing code can not handle select,radio,checkbox values that start with '-', so the '-' is added in the command generation -->
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164 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
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165 <option value="no_filter" selected="true">No filter (analyze everything)</option>
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166 <option value="del">Analyze deletions only </option>
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167 <option value="ins">Analyze insertions only </option>
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168 <option value="mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
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169 <option value="snp">Only SNPs (single nucleotide polymorphisms) </option>
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170 </param>
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171
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172 <param name="annotations" type="select" display="checkboxes" multiple="true" optional="true" label="Annotation options">
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173 <option value="cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option>
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174 <option value="canon">Only use canonical transcripts.</option>
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175 <option value="geneId">Use gene ID instead of gene name (VCF output). Default: false</option>
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176 <option value="hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option>
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177 <option value="lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option>
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178 <option value="oicr">Add OICR tag in VCF file. Default: false</option>
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179 <option value="onlyReg">Only use regulation tracks.</option>
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180 <option value="sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option>
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181 </param>
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182
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183 <param name="regulation" type="select" display="checkboxes" multiple="true" optional="true" label="Non-coding and regulatory Annotation">
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184 <help>These are available for only a few genomes</help>
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185 <!--GENOME REG_NAME -->
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186 <options from_file="snpeffect_regulationdb.loc">
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187 <column name="name" index="1"/>
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188 <column name="value" index="0"/>
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189 <filter type="param_value" ref="genomeVersion" key="name" column="1" />
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190 </options>
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191 </param>
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192
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193 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
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194 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/>
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195
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196 <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="true" label="Filter output">
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197 <option value="no-downstream">Do not show DOWNSTREAM changes </option>
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198 <option value="no-intergenic">Do not show INTERGENIC changes </option>
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199 <option value="no-intron">Do not show INTRON changes </option>
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200 <option value="no-upstream">Do not show UPSTREAM changes </option>
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201 <option value="no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
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202 </param>
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203
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204 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
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205 <option value="" selected="true">Use default (based on input type)</option>
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206 <option value="0">Force zero-based positions (both input and output)</option>
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207 <option value="1">Force one-based positions (both input and output)</option>
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208 </param>
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209 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name" help="By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. You can prepend any string you want to the chromosome name.">
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210 <validator type="regex" message="No whitespace allows">^\S*$</validator>
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211
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212 </param>
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213 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
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214 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
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215 </inputs>
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216 <outputs>
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217 <data format="vcf" name="snpeff_output" >
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218 <change_format>
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219 <when input="outputFormat" value="vcf" format="vcf" />
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220 <when input="outputFormat" value="txt" format="tabular" />
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221 <when input="outputFormat" value="bed" format="bed" />
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222 <when input="outputFormat" value="bedAnn" format="bed" />
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223 </change_format>
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224 </data>
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225
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226 <data format="html" name="statsFile">
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227 <filter>generate_stats == True</filter>
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228 </data>
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229 </outputs>
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230 <stdio>
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231 <exit_code range="1:" level="fatal" description="Error" />
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232 <exit_code range="-1" level="fatal" description="Error: Cannot open file" />
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233 </stdio>
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234 <tests>
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235 <test>
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236 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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237 <param name="inputFormat" value="vcf"/>
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238 <param name="outputFormat" value="vcf"/>
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239 <param name="genomeVersion" value="testCase"/>
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240 <param name="udLength" value="0"/>
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241 <param name="filterHomHet" value="no_filter"/>
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242 <param name="filterIn" value="no_filter"/>
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243 <param name="generate_stats" value="False"/>
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244 <!--
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245 <param name="filterOut" value="no-upstream"/>
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246 -->
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247 <output name="snpeff_output">
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248 <assert_contents>
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249 <!-- Check that an effect was added -->
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250 <has_text text="EFF=" />
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251 </assert_contents>
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252 </output>
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253 <!-- Check for a HTML header indicating that this was successful -->
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254 <!--
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255 <output name="statsFile">
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256 <assert_contents>
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257 <has_text text="SnpEff: Variant analysis" />
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258 </assert_contents>
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259 </output>
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260 -->
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261 </test>
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262
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263 <test>
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264 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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265 <param name="inputFormat" value="vcf"/>
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266 <param name="outputFormat" value="vcf"/>
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267 <param name="genomeVersion" value="testCase"/>
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268 <param name="udLength" value="0"/>
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269 <param name="filterHomHet" value="het"/>
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270 <param name="filterIn" value="no_filter"/>
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271 <!--
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272 <param name="filterOut" value=""/>
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273 -->
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274 <param name="generate_stats" value="False"/>
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275 <output name="snpeff_output">
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276 <assert_contents>
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277 <!-- Check that NO effects were added since -het is set -->
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278 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
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279 </assert_contents>
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280 </output>
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281 </test>
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282 <test>
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283 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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284 <param name="inputFormat" value="vcf"/>
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285 <param name="outputFormat" value="vcf"/>
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286 <param name="genomeVersion" value="testCase"/>
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287 <param name="udLength" value="0"/>
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288 <param name="filterHomHet" value="no_filter"/>
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289 <param name="filterIn" value="del"/>
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290 <!--
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291 <param name="filterOut" value=""/>
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292 -->
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293 <param name="generate_stats" value="False"/>
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294 <output name="snpeff_output">
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295 <assert_contents>
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296 <!-- Check that deleletions were evaluated -->
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297 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
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298 <!-- Check that insertion on last line was NOT evaluated -->
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299 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
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300 </assert_contents>
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301 </output>
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302 </test>
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303 <test>
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304 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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305 <param name="inputFormat" value="vcf"/>
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306 <param name="outputFormat" value="vcf"/>
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307 <param name="genomeVersion" value="testCase"/>
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308 <param name="udLength" value="0"/>
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309 <param name="filterHomHet" value="no_filter"/>
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310 <param name="filterIn" value="no_filter"/>
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311 <param name="filterOut" value="no-upstream"/>
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312 <param name="generate_stats" value="False"/>
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313 <output name="snpeff_output">
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314 <assert_contents>
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315 <!-- Check that NO UPSTREAM effect was added -->
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316 <not_has_text text="UPSTREAM" />
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317 </assert_contents>
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318 </output>
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319 </test>
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320
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321 </tests>
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322 <help>
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323
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324 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
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325
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326 For details about this tool, please see the snpEff_ web site.
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327
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328 .. _snpEff: http://snpEff.sourceforge.net
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329 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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330 </help>
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331 </tool>
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332
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