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1 <tool id="snpEff" name="SnpEff" version="3.6">
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2 <description>Variant effect and annotation</description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>snpEff_macros.xml</import>
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6 </macros>
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7 <command>
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8 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
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9 -c \$SNPEFF_JAR_PATH/snpEff.config
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10 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
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11 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
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12 -spliceSiteSize $spliceSiteSize
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13 #end if
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14 #if $filterIn and $filterIn.__str__ != 'no_filter':
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15 $filterIn
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16 #end if
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17 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
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18 $filterHomHet
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19 #end if
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20 #if $annotations and $annotations.__str__ != '':
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21 #echo " "
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22 #echo ' '.join($annotations.__str__.split(','))
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23 #end if
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24 #if $filterOut and $filterOut.__str__ != '':
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25 #echo " "
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26 #echo ' '.join($filterOut.__str__.split(','))
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27 #end if
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28 #if str( $transcripts ) != 'None':
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29 -onlyTr $transcripts
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30 #end if
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31 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
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32 -interval $intervals
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33 #end if
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34 #if $statsFile:
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35 -stats $statsFile
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36 #end if
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37 #if $offset.__str__ != '':
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38 ${offset}
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39 #end if
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40 #if $chr.__str__.strip() != '':
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41 -chr "$chr"
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42 #end if
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43 $noLog
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44 #if $snpDb.genomeSrc == 'cached':
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45 -dataDir ${snpDb.genomeVersion.fields.path}
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46 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
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47 #echo " "
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48 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
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49 #end if
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50 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
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51 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
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52 #end if
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53 $snpDb.genomeVersion
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54 #elif $snpDb.genomeSrc == 'history':
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55 -dataDir ${snpDb.snpeff_db.files_path}
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56 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
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57 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
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58 #echo " "
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59 #echo ' -'.join($xannotations)
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60 #end if
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61 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
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62 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
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63 #end if
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64 ${snpDb.snpeff_db.metadata.genome_version}
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65 #else
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66 -download
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67 $snpDb.genome_version
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68 #end if
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69 $input > $snpeff_output ;
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70 #if $statsFile:
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71 #import os
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72 #set $genes_file = str($statsFile) + '.genes.txt'
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73 #set $genes_file_name = os.path.split($genes_file)[-1]
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74 mkdir $statsFile.files_path;
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75 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
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76 #end if
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77 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
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78 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
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79 sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
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80 #end if
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81 </command>
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82 <inputs>
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83 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
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84
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85 <param name="inputFormat" type="select" label="Input format">
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86 <option value="vcf" selected="true">VCF</option>
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87 <option value="txt">Tabular (Deprecated)</option>
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88 <option value="pileup">Pileup (Deprecated)</option>
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89 <option value="bed">BED (Deprecated)</option>
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90 </param>
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91
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92 <conditional name="outputConditional">
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93 <param name="outputFormat" type="select" label="Output format">
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94 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
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95 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
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96 <option value="txt">Tabular</option>
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97 <option value="bed">BED</option>
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98 <option value="bedAnn">BED annotations</option>
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99 </param>
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100 <when value="vcf" />
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101 <when value="gatk">
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102 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
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103 </when>
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104 <when value="txt" />
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105 <when value="bed" />
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106 <when value="bedAnn" />
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107 </conditional>
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108
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109 <conditional name="snpDb">
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110 <param name="genomeSrc" type="select" label="Genome source">
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111 <option value="cached">Locally installed reference genome</option>
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112 <option value="history">Reference genome from your history</option>
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113 <option value="named">Named on demand</option>
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114 </param>
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115 <when value="cached">
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116 <param name="genomeVersion" type="select" label="Genome">
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117 <!--GENOME DESCRIPTION-->
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118 <options from_data_table="snpeff_genomedb">
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119 <filter type="unique_value" column="0" />
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120 </options>
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121 </param>
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122 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
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123 <help>These are available for only a few genomes</help>
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124 <options from_data_table="snpeff_annotations">
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125 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
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126 <filter type="unique_value" column="1" />
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127 </options>
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128 </param>
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129 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
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130 <help>These are available for only a few genomes</help>
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131 <options from_data_table="snpeff_regulationdb">
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132 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
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133 <filter type="unique_value" column="1" />
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134 </options>
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135 </param>
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136 </when>
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137 <when value="history">
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138 <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
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139 <!-- From metadata -->
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140 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
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141 <help>These are available for only a few genomes</help>
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142 <options>
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143 <filter type="data_meta" ref="snpeff_db" key="annotation" />
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144 </options>
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145 </param>
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146 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
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147 <help>These are available for only a few genomes</help>
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148 <options>
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149 <filter type="data_meta" ref="snpeff_db" key="regulation" />
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150 </options>
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151 </param>
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152 </when>
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153 <when value="named">
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154 <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/>
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155 </when>
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156 </conditional>
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157
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158 <param name="udLength" type="select" label="Upstream / Downstream length">
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159 <option value="0">No upstream / downstream intervals (0 bases)</option>
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160 <option value="200">200 bases</option>
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161 <option value="500">500 bases</option>
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162 <option value="1000">1000 bases</option>
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163 <option value="2000">2000 bases</option>
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164 <option value="5000" selected="true">5000 bases</option>
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165 <option value="10000">10000 bases</option>
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166 <option value="20000">20000 bases</option>
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167 </param>
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168
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169 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
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170 <option value="1">1 base</option>
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171 <option value="2" selected="true">2 bases</option>
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172 <option value="3">3 bases</option>
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173 <option value="4">4 bases</option>
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174 <option value="5">5 bases</option>
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175 <option value="6">6 bases</option>
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176 <option value="7">7 bases</option>
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177 <option value="8">8 bases</option>
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178 <option value="9">9 bases</option>
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179 </param>
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180
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181 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
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182 <option value="no_filter" selected="true">No filter (analyze everything)</option>
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183 <option value="-hom">Analyze homozygous sequence changes only</option>
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184 <option value="-het">Analyze heterozygous sequence changes only</option>
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185 </param>
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186
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187 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
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188 <option value="no_filter" selected="true">No filter (analyze everything)</option>
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189 <option value="-del">Analyze deletions only</option>
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190 <option value="-ins">Analyze insertions only</option>
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191 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option>
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192 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option>
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193 </param>
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194
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195 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
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196 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
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197 <option value="-canon">Only use canonical transcripts</option>
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198 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
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199 <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option>
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200 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
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201 <option value="-oicr">Add OICR tag in VCF file</option>
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202 <option value="-onlyReg">Only use regulation tracks</option>
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203 <option value="-sequenceOntolgy">Use Sequence Ontology terms</option>
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204 </param>
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205 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
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206 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/>
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207 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
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208 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
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209 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
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210 <option value="-no-intron">Do not show INTRON changes</option>
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211 <option value="-no-upstream">Do not show UPSTREAM changes</option>
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212 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
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213 </param>
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214
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215 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
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216 <option value="" selected="true">Use default (based on input type)</option>
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217 <option value="-0">Force zero-based positions (both input and output)</option>
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218 <option value="-1">Force one-based positions (both input and output)</option>
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219 </param>
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220 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
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221 <help>
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222 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
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223 You can prepend any string you want to the chromosome name.
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224 </help>
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225 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
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226 </param>
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227 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
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228 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
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229 </inputs>
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230 <outputs>
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231 <data format="vcf" name="snpeff_output" >
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232 <change_format>
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233 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
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234 <when input="outputConditional.outputFormat" value="bed" format="bed" />
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235 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
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236 </change_format>
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237 </data>
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238 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
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239 <filter>generate_stats == True</filter>
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240 </data>
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241 </outputs>
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242 <expand macro="stdio" />
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243 <tests>
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244 <!-- Check that an effect was added in out VCF -->
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245 <!-- Check for a HTML header indicating that this was successful -->
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246 <!--
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247 <output name="statsFile">
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248 <assert_contents>
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249 <has_text text="SnpEff: Variant analysis" />
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250 </assert_contents>
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251 </output>
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252 -->
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253 <!-- Setting filterOut throws exception in twilltestcase.py
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254 <test>
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255 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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256 <param name="inputFormat" value="vcf"/>
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257 <param name="outputFormat" value="vcf"/>
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258 <param name="genomeSrc" value="named"/>
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259 <param name="genome_version" value="testCase"/>
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260 <param name="udLength" value="0"/>
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261 <param name="filterHomHet" value="no_filter"/>
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262 <param name="filterIn" value="no_filter"/>
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263 <param name="generate_stats" value="False"/>
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264 <param name="filterOut" value="+-no-upstream"/>
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265 <output name="snpeff_output">
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266 <assert_contents>
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267 <has_text text="EFF=" />
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268 </assert_contents>
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269 </output>
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270 </test>
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271 -->
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272
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273 <test>
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274 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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275 <param name="inputFormat" value="vcf"/>
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276 <param name="outputFormat" value="vcf"/>
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277 <param name="genomeSrc" value="named"/>
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278 <param name="genome_version" value="testCase"/>
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279 <param name="udLength" value="0"/>
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280 <param name="filterHomHet" value="+-het"/>
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281 <param name="filterIn" value="no_filter"/>
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282 <!--
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283 <param name="filterOut" value=""/>
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284 -->
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285 <param name="generate_stats" value="False"/>
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286 <output name="snpeff_output">
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287 <assert_contents>
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288 <!-- Check that NO effects were added since -het is set -->
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289 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
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290 </assert_contents>
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291 </output>
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292 </test>
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293
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294 <test>
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295 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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296 <param name="inputFormat" value="vcf"/>
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297 <param name="outputFormat" value="vcf"/>
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298 <param name="genomeSrc" value="named"/>
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299 <param name="genome_version" value="testCase"/>
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300 <param name="udLength" value="0"/>
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301 <param name="filterHomHet" value="no_filter"/>
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302 <param name="filterIn" value="+-del"/>
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303 <!--
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304 <param name="filterOut" value=""/>
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305 -->
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306 <param name="generate_stats" value="False"/>
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307 <output name="snpeff_output">
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308 <assert_contents>
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309 <!-- Check that deleletions were evaluated -->
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310 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
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311 <!-- Check that insertion on last line was NOT evaluated -->
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312 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
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313 </assert_contents>
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314 </output>
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315 </test>
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316
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317 <!-- Check that NO UPSTREAM effect was added -->
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318 <!-- Setting filterOut throws exception in twilltestcase.py
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319 <test>
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320 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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321 <param name="inputFormat" value="vcf"/>
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322 <param name="outputFormat" value="vcf"/>
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323 <param name="genomeSrc" value="named"/>
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324 <param name="genome_version" value="testCase"/>
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325 <param name="udLength" value="0"/>
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326 <param name="filterHomHet" value="no_filter"/>
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327 <param name="filterIn" value="no_filter"/>
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328 <param name="filterOut" value="+-no-upstream"/>
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329 <param name="generate_stats" value="False"/>
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330 <output name="snpeff_output">
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331 <assert_contents>
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332 <not_has_text text="UPSTREAM" />
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333 </assert_contents>
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334 </output>
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335 </test>
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336 -->
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337
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338 </tests>
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339 <help>
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340 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
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341
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342 @EXTERNAL_DOCUMENTATION@
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343
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344 </help>
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345 <expand macro="citations" />
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346 </tool>
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347
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