Mercurial > repos > jjohnson > snpeff

annotate snpEff.xml @ 23:924af057bbca draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:51:40 -0400
parents bb0797deab78
children
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1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
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2 <description>Variant effect and annotation</description>
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3 <macros>
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4 <import>snpEff_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
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12 -c "\$SNPEFF_JAR_PATH/snpEff.config"
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13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
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14 #if $spliceSiteSize and str($spliceSiteSize) != '':
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15 -spliceSiteSize "$spliceSiteSize"
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16 #end if
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17 #if $spliceRegion.setSpliceRegions == 'yes':
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18 #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '':
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19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
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20 #end if
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21 #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '':
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22 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
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23 #end if
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24 #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '':
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25 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
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26 #end if
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27 #end if
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28 #if $annotations and str($annotations) != '':
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29 #echo " "
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30 #echo ' '.join(str($annotations).split(','))
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31 #end if
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32 #if $filterOut and str($filterOut) != '':
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33 #echo " "
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34 #echo ' '.join(str($filterOut).split(','))
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35 #end if
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36 #if $filter.specificEffects == 'yes' and $filter.effects:
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37 #for $eff in str($filter.effects).split(','):
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38 -no $eff
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39 #end for
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40 #end if
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41 #if str( $transcripts ) != 'None':
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42 -onlyTr $transcripts
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43 #end if
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44 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
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45 -interval $intervals
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46 #end if
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47 #if $statsFile:
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48 -stats $statsFile
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49 #end if
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50 #if str($offset) != 'default':
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51 ${offset}
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52 #end if
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53 #if str($chr).strip() != '':
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54 -chr "$chr"
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55 #end if
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56 $noLog
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57 #if $snpDb.genomeSrc == 'cached':
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58 -dataDir ${snpDb.genomeVersion.fields.path}
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59 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
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60 #echo " "
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61 #echo ' '.join(str($snpDb.extra_annotations).split(','))
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62 #end if
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63 #if $snpDb.regulation and str($snpDb.regulation) != '':
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64 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
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65 #end if
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66 $snpDb.genomeVersion
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67 #elif $snpDb.genomeSrc == 'history':
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68 -dataDir ${snpDb.snpeff_db.extra_files_path}
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69 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
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70 #set xannotations = [' '] + str($snpDb.extra_annotations).split(',')
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71 #echo " "
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72 #echo ' -'.join($xannotations)
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73 #end if
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74 #if $snpDb.regulation and str($snpDb.regulation) != '':
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75 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
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76 #end if
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77 ${snpDb.snpeff_db.metadata.genome_version}
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78 #else
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79 -download
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80 $snpDb.genome_version
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81 #end if
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82 "$input" > "$snpeff_output";
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83 #if $statsFile:
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84 #import os
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85 #set $genes_file = str($statsFile) + '.genes.txt'
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86 #set $genes_file_name = os.path.split($genes_file)[-1]
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87 mkdir $statsFile.files_path;
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88 mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#;
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89 #end if
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90 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
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91 ## 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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92 sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
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93 #end if
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94 ]]>
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95 </command>
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96 <inputs>
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97 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
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98
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99 <param name="inputFormat" type="select" label="Input format">
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100 <option value="vcf" selected="true">VCF</option>
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101 <option value="bed">BED (Deprecated)</option>
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102 </param>
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103
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104 <conditional name="outputConditional">
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105 <param name="outputFormat" type="select" label="Output format">
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106 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
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107 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
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108 <option value="bed">BED</option>
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109 <option value="bedAnn">BED annotations</option>
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110 </param>
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111 <when value="vcf" />
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112 <when value="gatk">
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113 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
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114 </when>
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115 <when value="bed" />
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116 <when value="bedAnn" />
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117 </conditional>
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118
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119 <conditional name="snpDb">
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120 <param name="genomeSrc" type="select" label="Genome source">
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121 <option value="cached">Locally installed reference genome</option>
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122 <option value="history">Reference genome from your history</option>
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123 <option value="named">Named on demand</option>
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124 </param>
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125 <when value="cached">
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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_data_table="snpeffv_genomedb">
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129 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
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130 <filter type="unique_value" column="2" />
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131 </options>
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132 </param>
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133 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
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134 <help>These are available for only a few genomes</help>
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135 <options from_data_table="snpeffv_annotations">
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136 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
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137 <filter type="unique_value" column="3" />
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138 </options>
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139 </param>
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140 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
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141 <help>These are available for only a few genomes</help>
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142 <options from_data_table="snpeffv_regulationdb">
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143 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
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144 <filter type="unique_value" column="3" />
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145 </options>
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146 </param>
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147 </when>
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148 <when value="history">
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149 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
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150 <options options_filter_attribute="metadata.snpeff_version" >
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151 <filter type="add_value" value="@SNPEFF_VERSION@" />
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152 </options>
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153 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ Genome databases.">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
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154 </param>
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155 <!-- From metadata -->
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156 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
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157 <help>These are available for only a few genomes</help>
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158 <options>
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159 <filter type="data_meta" ref="snpeff_db" key="annotation" />
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160 </options>
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161 </param>
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162 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
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163 <help>These are available for only a few genomes</help>
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164 <options>
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165 <filter type="data_meta" ref="snpeff_db" key="regulation" />
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166 </options>
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167 </param>
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168 </when>
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169 <when value="named">
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170 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
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171 <help>@SNPEFF_DATABASE_URL@</help>
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172 <validator type="regex" message="A genome version name is required">\S+</validator>
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173 </param>
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174 </when>
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175 </conditional>
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176
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177 <param name="udLength" type="select" label="Upstream / Downstream length">
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178 <option value="0">No upstream / downstream intervals (0 bases)</option>
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179 <option value="200">200 bases</option>
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180 <option value="500">500 bases</option>
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181 <option value="1000">1000 bases</option>
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182 <option value="2000">2000 bases</option>
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183 <option value="5000" selected="true">5000 bases</option>
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184 <option value="10000">10000 bases</option>
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185 <option value="20000">20000 bases</option>
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186 </param>
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187
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188 <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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189 <option value="1">1 base</option>
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190 <option value="2" selected="true">2 bases</option>
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191 <option value="3">3 bases</option>
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192 <option value="4">4 bases</option>
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193 <option value="5">5 bases</option>
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194 <option value="6">6 bases</option>
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195 <option value="7">7 bases</option>
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196 <option value="8">8 bases</option>
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197 <option value="9">9 bases</option>
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198 </param>
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199
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200 <conditional name="spliceRegion">
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201 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
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202 <option value="no">Use Defaults</option>
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203 <option value="yes">Set Splice Region Parameters</option>
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204 </param>
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205 <when value="no"/>
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206 <when value="yes">
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207 <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/>
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208 <param name="spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases"/>
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209 <param name="spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases"/>
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210 </when>
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211 </conditional>
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212
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213 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
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214 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
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215 <option value="-canon">Only use canonical transcripts</option>
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216 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
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217 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
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218 <option value="-oicr">Add OICR tag in VCF file</option>
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219 <option value="-onlyReg">Only use regulation tracks</option>
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220 <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
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221 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
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222 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
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223 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
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224 <option value="-noHgvs">Do not add HGVS annotations.</option>
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225 <option value="-noLof">Do not add LOF and NMD annotations.</option>
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226 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
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227 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
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228 </param>
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229 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
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230 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
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231 <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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232 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
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233 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
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234 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
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235 <option value="-no-intron">Do not show INTRON changes</option>
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236 <option value="-no-upstream">Do not show UPSTREAM changes</option>
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237 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
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238 </param>
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239 <conditional name="filter">
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240 <param name="specificEffects" type="select" label="Filter out specific Effects">
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241 <option value="no">No</option>
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242 <option value="yes">Yes</option>
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243 </param>
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244 <when value="no"/>
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245 <when value="yes">
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246 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects">
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247 <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option>
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248 <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option>
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249 <option value="CODON_CHANGE">CODON_CHANGE (coding_sequence_variant) One or many codons are changed e.g.: An MNP of size multiple of 3 MODERATE</option>
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250 <option value="CODON_INSERTION">CODON_INSERTION (inframe_insertion) One or many codons are inserted e.g.: An insert multiple of three in a codon boundary MODERATE</option>
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251 <option value="CODON_CHANGE_PLUS_CODON_INSERTION">CODON_CHANGE_PLUS_CODON_INSERTION (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary MODERATE</option>
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252 <option value="CODON_DELETION">CODON_DELETION (inframe_deletion) One or many codons are deleted e.g.: A deletion multiple of three at codon boundary MODERATE</option>
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253 <option value="CODON_CHANGE_PLUS_CODON_DELETION">CODON_CHANGE_PLUS_CODON_DELETION (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary MODERATE</option>
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254 <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option>
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255 <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option>
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256 <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option>
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257 <option value="FRAME_SHIFT">FRAME_SHIFT (frameshift_variant) Insertion or deletion causes a frame shift e.g.: An indel size is not multple of 3 HIGH</option>
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258 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
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259 <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option>
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260 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option>
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261 <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option>
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262 <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option>
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263 <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option>
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264 <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option>
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265 <option value="NON_SYNONYMOUS_CODING">NON_SYNONYMOUS_CODING (missense_variant) Variant causes a codon that produces a different amino acid e.g.: Tgg/Cgg, W/R MODERATE</option>
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266 <option value="NON_SYNONYMOUS_START">NON_SYNONYMOUS_START (initiator_codon_variant) Variant causes start codon to be mutated into another start codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
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267 <option value="NON_SYNONYMOUS_STOP">NON_SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
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268 <option value="RARE_AMINO_ACID">RARE_AMINO_ACID (rare_amino_acid_variant) The variant hits a rare amino acid thus is likely to produce protein loss of function HIGH</option>
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269 <option value="SPLICE_SITE_ACCEPTOR">SPLICE_SITE_ACCEPTOR (splice_acceptor_variant) The variant hits a splice acceptor site (defined as two bases before exon start, except for the first exon). HIGH</option>
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270 <option value="SPLICE_SITE_DONOR">SPLICE_SITE_DONOR (splice_donor_variant) The variant hits a Splice donor site (defined as two bases after coding exon end, except for the last exon). HIGH</option>
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271 <option value="SPLICE_SITE_REGION">SPLICE_SITE_REGION (splice_region_variant) A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. LOW</option>
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272 <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option>
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273 <option value="SPLICE_SITE_BRANCH_U12">SPLICE_SITE_BRANCH_U12 (splice_region_variant) A varaint affective putative (Lariat) branch point from U12 splicing machinery, located in the intron. MODERATE</option>
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274 <option value="STOP_LOST">STOP_LOST (stop_lost) Variant causes stop codon to be mutated into a non-stop codon e.g.: Tga/Cga, */R HIGH</option>
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275 <option value="START_GAINED">START_GAINED (5_prime_UTR_premature start_codon_gain_variant) A variant in 5'UTR region produces a three base sequence that can be a START codon. LOW</option>
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276 <option value="START_LOST">START_LOST (start_lost) Variant causes start codon to be mutated into a non-start codon. e.g.: aTg/aGg, M/R HIGH</option>
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277 <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option>
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278 <option value="SYNONYMOUS_CODING">SYNONYMOUS_CODING (synonymous_variant) Variant causes a codon that produces the same amino acid e.g.: Ttg/Ctg, L/L LOW</option>
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279 <option value="SYNONYMOUS_START">SYNONYMOUS_START (start_retained) Variant causes start codon to be mutated into another start codon. e.g.: Ttg/Ctg, L/L (TTG and CTG can be START codons) LOW</option>
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280 <option value="SYNONYMOUS_STOP">SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon. e.g.: taA/taG, */* LOW</option>
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281 <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>
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282 <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>
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283 <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>
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284 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
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285 <option value="UTR_3_DELETED">UTR_3_DELETED (3_prime_UTR_truncation + exon_loss) The variant deletes an exon which is in the 3'UTR of the transcript MODERATE</option>
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286 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
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287 <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript MODERATE</option>
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288 <option value="NEXT_PROT">NEXT_PROT (sequence_feature + exon_loss_variant) A 'NextProt' based annotation. Details are provided in the 'feature type' sub-field (ANN), or in the effect details (EFF). MODERATE </option>
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289
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290 </param>
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291 </when>
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292 </conditional>
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293
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294 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
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295 <option value="default" selected="true">Use default (based on input type)</option>
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296 <option value="-0">Force zero-based positions (both input and output)</option>
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297 <option value="-1">Force one-based positions (both input and output)</option>
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298 </param>
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299 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
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300 <help>
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301 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
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302 You can prepend any string you want to the chromosome name.
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303 </help>
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304 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
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305 </param>
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306 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
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307 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
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308 </inputs>
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309 <outputs>
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310 <data format="vcf" name="snpeff_output" >
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311 <change_format>
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312 <when input="outputConditional.outputFormat" value="bed" format="bed" />
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313 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
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314 </change_format>
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315 </data>
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316 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
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317 <filter>generate_stats == True</filter>
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318 </data>
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319 </outputs>
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320 <tests>
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321 <!-- Check that an effect was added in out VCF -->
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322 <!-- Check for a HTML header indicating that this was successful -->
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323 <!--
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324 <output name="statsFile">
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325 <assert_contents>
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326 <has_text text="SnpEff: Variant analysis" />
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327 </assert_contents>
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328 </output>
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329 -->
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330 <!-- Setting filterOut throws exception in twilltestcase.py
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331 <test>
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332 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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333 <param name="inputFormat" value="vcf"/>
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334 <param name="outputFormat" value="vcf"/>
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335 <param name="genomeSrc" value="named"/>
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336 <param name="genome_version" value="testCase"/>
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337 <param name="udLength" value="0"/>
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338 <param name="generate_stats" value="False"/>
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339 <param name="filterOut" value="+-no-upstream"/>
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340 <output name="snpeff_output">
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341 <assert_contents>
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342 <has_text text="EFF=" />
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343 </assert_contents>
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344 </output>
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345 </test>
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346 -->
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347
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348 <test>
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349 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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350 <param name="inputFormat" value="vcf"/>
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351 <param name="outputFormat" value="vcf"/>
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352 <param name="genomeSrc" value="named"/>
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353 <param name="genome_version" value="testCase"/>
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354 <param name="udLength" value="0"/>
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355 <!--
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356 <param name="filterOut" value=""/>
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357 -->
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358 <param name="generate_stats" value="False"/>
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359 <output name="snpeff_output">
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360 <assert_contents>
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361 <!-- Check that deleletions were evaluated -->
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362 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
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363 <!-- Check that insertion on last line was NOT evaluated -->
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364 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
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365 </assert_contents>
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366 </output>
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367 </test>
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368
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369 <!-- Check that NO UPSTREAM effect was added -->
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370 <!-- Setting filterOut throws exception in twilltestcase.py
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371 <test>
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372 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
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373 <param name="inputFormat" value="vcf"/>
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374 <param name="outputFormat" value="vcf"/>
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375 <param name="genomeSrc" value="named"/>
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376 <param name="genome_version" value="testCase"/>
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377 <param name="udLength" value="0"/>
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378 <param name="filterOut" value="+-no-upstream"/>
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379 <param name="generate_stats" value="False"/>
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380 <output name="snpeff_output">
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381 <assert_contents>
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382 <not_has_text text="UPSTREAM" />
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383 </assert_contents>
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384 </output>
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385 </test>
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386 -->
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387
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388 </tests>
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389 <help><![CDATA[
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390
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391 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
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392
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393 @EXTERNAL_DOCUMENTATION@
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394
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395 ]]>
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396 </help>
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397 <expand macro="citations" />
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398 </tool>
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399