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1 <tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0">
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2 <options sanitize="False" />
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3 <description>Filter variants using arbitrary expressions</description>
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4 <expand macro="requirements" />
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5 <macros>
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6 <import>snpSift_macros.xml</import>
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7 </macros>
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8 <command>
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9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse
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10 #if $filtering.mode == 'field':
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11 #if $filtering.replace.pass:
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12 --pass
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13 #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0:
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14 --filterId "$filtering.replace.filterId"
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15 #end if
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16 #end if
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17 #if $filtering.addFilter and len($filtering.addFilter.__str__.strip()) > 0:
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18 --addFilter "$filtering.addFilter"
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19 #end if
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20 #if $filtering.rmFilter and len($filtering.rmFilter.__str__.strip()) > 0:
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21 --rmFilter "$filtering.rmFilter"
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22 #end if
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23 #end if
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24 > $output
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25 </command>
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26 <inputs>
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27 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
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28 <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." />
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29 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
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30 <conditional name="filtering">
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31 <param name="mode" type="select" label="Filter mode">
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32 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
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33 <option value="field">Change the FILTER field, but retain all entries</option>
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34 </param>
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35 <when value="entries"/>
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36 <when value="field">
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37 <conditional name="replace">
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38 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
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39 help="appends an ID tag to non-matching entry FILTER "/>
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40 <when value="no"/>
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41 <when value="yes">
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42 <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10"
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43 help="Default ID is 'SnpSift'"/>
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44 </when>
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45 </conditional>
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46 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
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47 <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/>
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48 </when>
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49 </conditional>
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50 </inputs>
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51 <configfiles>
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52 <configfile name="exprFile">
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53 $expr#slurp
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54 </configfile>
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55 </configfiles>
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56
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57 <outputs>
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58 <data format="vcf" name="output" />
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59 </outputs>
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60 <expand macro="stdio" />
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61 <tests>
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62 <test>
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63 <param name="input" ftype="vcf" value="test01.vcf"/>
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64 <param name="expr" value="QUAL >= 50"/>
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65 <param name="mode" value="entries"/>
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66 <output name="output">
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67 <assert_contents>
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68 <has_text text="28837706" />
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69 <not_has_text text="NT_166464" />
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70 </assert_contents>
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71 </output>
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72 </test>
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73
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74 <test>
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75 <param name="input" ftype="vcf" value="test01.vcf"/>
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76 <param name="expr" value="(CHROM = '19')"/>
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77 <param name="mode" value="entries"/>
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78 <output name="output">
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79 <assert_contents>
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80 <has_text text="3205820" />
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81 <not_has_text text="NT_16" />
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82 </assert_contents>
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83 </output>
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84 </test>
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85
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86 <test>
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87 <param name="input" ftype="vcf" value="test01.vcf"/>
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88 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/>
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89 <param name="mode" value="entries"/>
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90 <output name="output">
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91 <assert_contents>
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92 <has_text text="20175" />
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93 <has_text text="35549" />
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94 <has_text text="22256" />
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95 <not_has_text text="18933" />
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96 <not_has_text text="37567" />
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97 </assert_contents>
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98 </output>
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99 </test>
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100
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101 <test>
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102 <param name="input" ftype="vcf" value="test01.vcf"/>
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103 <param name="expr" value="( DP >= 5 )"/>
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104 <param name="mode" value="entries"/>
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105 <output name="output">
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106 <assert_contents>
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107 <has_text text="DP=5;" />
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108 <has_text text="DP=6;" />
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109 <not_has_text text="DP=1;" />
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110 </assert_contents>
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111 </output>
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112 </test>
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113 </tests>
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114 <help>
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115
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116 **SnpSift filter**
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117
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118 You can filter a VCF file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.
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119
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120 Some examples:
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121
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122 - *I want just the variants from the second million bases of chr1*:
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123
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124 ::
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125
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126 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
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127
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128 - *Filter value is either 'PASS' or it is missing*:
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129
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130 ::
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131
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132 (FILTER = 'PASS') | ( na FILTER )
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133
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134 - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
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135
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136 ::
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137
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138 ( EFF[*].EFFECT = 'frameshift_variant' )
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139
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140 - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
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141
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142 ::
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143
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144 ( EFF[*].EFFECT = 'FRAME_SHIFT' )
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145
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146 - *I want to filter out samples with quality less than 30*:
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147
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148 ::
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149
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150 ( QUAL > 30 )
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151
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152 - *...but we also want InDels that have quality 20 or more*:
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153
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154 ::
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155
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156 (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
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157
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158 - *...or any homozygous variant present in more than 3 samples*:
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159
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160 ::
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161
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162 (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
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163
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164 - *...or any heterozygous sample with coverage 25 or more*:
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165
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166 ::
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167
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168 ((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
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169
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170 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
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171
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172 ::
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173
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174 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
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175
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176
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177 **For information regarding HGVS and Sequence Ontology terms versus classic names**:
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178
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179 - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
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180 - http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect
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181
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182
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183 @EXTERNAL_DOCUMENTATION@
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184 http://snpeff.sourceforge.net/SnpSift.html#filter
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185
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186 @CITATION_SECTION@
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187
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188 </help>
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189 </tool>
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