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1 <tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1">
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2 <description></description>
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3 <macros>
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4 <import>gatk2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command interpreter="python">
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9 #from binascii import hexlify
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10
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11 gatk2_wrapper.py
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12 --stdout "${output_log}"
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13 #for $var_count, $variant in enumerate( $reference_source.input_variants ):
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14 -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
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15 #end for
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16 -p '
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17 @JAR_PATH@
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18 -T "VariantEval"
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19 --out "${output_report}"
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20 \$GATK2_SITE_OPTIONS
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21
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22 @THREADS@
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23
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24 #if $reference_source.reference_source_selector != "history":
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25 -R "${reference_source.ref_file.fields.path}"
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26 #end if
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27 '
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28
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29 #for $rod_binding in $comp_rod_bind:
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30 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
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31 #if str( $rod_binding.comp_known_names ):
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32 -p '--known_names "${rod_binding.comp_rod_name}"'
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33 #end if
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34 #end for
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35
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36 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
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37 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
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38 #if $dbsnp_rod_bind_type.dbsnp_known_names
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39 -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
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40 #end if
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41 #end if
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42
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43 #include source=$standard_gatk_options#
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44
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45 ##start analysis specific options
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46 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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47 #for $stratification in $analysis_param_type.stratifications:
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48 #set $select_string = "--select_exps '%s' --select_names '%s'" % ( str( $stratification.select_exps ), str( $stratification.select_name ) )
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49 -o '${ hexlify( $select_string ) }'
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50 #end for
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51 -p '
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52
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53 #for $sample in $analysis_param_type.samples:
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54 --sample "${sample.sample}"
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55 #end for
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56
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57 #if str( $analysis_param_type.stratification_modules ) != "None":
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58 #for $stratification_module in str( $analysis_param_type.stratification_modules).split( ',' ):
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59 --stratificationModule "${stratification_module}"
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60 #end for
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61 #end if
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62
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63 ${analysis_param_type.do_not_use_all_standard_stratifications}
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64
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65 #for $variant_type in $analysis_param_type.only_variants_of_type:
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66 --onlyVariantsOfType "${variant_type.variant_type}"
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67 #end for
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68
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69 #if str( $analysis_param_type.eval_modules ) != "None":
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70 #for $eval_module in str( $analysis_param_type.eval_modules).split( ',' ):
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71 --evalModule "${eval_module}"
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72 #end for
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73 #end if
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74
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75 ${analysis_param_type.do_not_use_all_standard_modules}
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76
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77 #if str( $analysis_param_type.num_samples ) != "0":
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78 --numSamples "${analysis_param_type.num_samples}"
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79 #end if
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80
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81 --minPhaseQuality "${analysis_param_type.min_phase_quality}"
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82
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83 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
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84
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85 #if str( $analysis_param_type.ancestral_alignments ) != "None":
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86 --ancestralAlignments "${analysis_param_type.ancestral_alignments}"
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87 #end if
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88 '
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89 #if str( $analysis_param_type.known_cnvs ) != "None":
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90 -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs"
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91 #end if
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92
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93 #if str( $analysis_param_type.strat_intervals ) != "None":
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94 -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals"
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95 #end if
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96 #end if
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97 </command>
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98 <inputs>
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99
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100 <conditional name="reference_source">
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101 <expand macro="reference_source_selector_param" />
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102 <when value="cached">
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103 <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;"/>
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104 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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105 <options from_data_table="gatk2_picard_indexes">
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106 <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
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107 </options>
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108 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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109 </param>
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110 </when>
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111 <when value="history"> <!-- FIX ME!!!! -->
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112 <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;" />
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113 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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114 </when>
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115 </conditional>
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116
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117 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &lt;comp&gt;">
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118 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
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119 <param name="comp_rod_name" type="text" value="" label="Comparison ROD name">
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120 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
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121 </param>
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122 <param name="comp_known_names" type="boolean" label="Use comparison ROD file as known_names" help="-knownName,--known_names &lt;known_names&gt;"/>
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123 </repeat>
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124 <conditional name="dbsnp_rod_bind_type">
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125 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &lt;dbsnp&gt;">
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126 <option value="set_dbsnp" selected="True">Set dbSNP</option>
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127 <option value="exclude_dbsnp">Don't set dbSNP</option>
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128 </param>
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129 <when value="exclude_dbsnp" />
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130 <when value="set_dbsnp">
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131 <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
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132 <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">
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133 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
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134 </param>
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135 <param name="dbsnp_known_names" type="boolean" label="Use dbSNP ROD file as known_names" help="-knownName,--known_names &lt;known_names&gt;" />
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136 </when>
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137 </conditional>
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138
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139 <expand macro="gatk_param_type_conditional" />
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140
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141 <expand macro="analysis_type_conditional">
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142 <repeat name="stratifications" title="Stratification">
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143 <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &lt;select_exps&gt;">
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144 <sanitizer>
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145 <valid initial="string.printable">
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146 <remove value="'"/>
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147 </valid>
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148 <mapping initial="none"/>
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149 </sanitizer>
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150 </param>
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151 <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &lt;select_names&gt;"/>
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152 </repeat>
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153
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154 <repeat name="samples" title="Sample" help="-sn,--sample &lt;sample&gt;">
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155 <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/>
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156 </repeat>
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157
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158 <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &lt;stratificationModule&gt;" >
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159 <option value="AlleleCount" />
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160 <option value="AlleleFrequency" />
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161 <option value="CompRod" />
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162 <option value="Contig" />
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163 <option value="CpG" />
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164 <option value="Degeneracy" />
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165 <option value="EvalRod" />
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166 <option value="Filter" />
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167 <option value="FunctionalClass" />
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168 <option value="IndelSize" />
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169 <option value="IntervalStratification" />
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170 <option value="JexlExpression" />
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171 <option value="Novelty" />
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172 <option value="OneBPIndel" />
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173 <option value="Sample" />
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174 <option value="SnpEffPositionModifier" />
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175 <option value="TandemRepeat" />
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176 <option value="VariantType" />
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177 </param>
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178 <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" />
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179
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180 <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
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181 <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
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182 </repeat>
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183
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184 <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &lt;evalModule&gt;" >
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185 <option value="CompOverlap" />
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186 <option value="CountVariants" />
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187 <option value="IndelLengthHistogram" />
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188 <option value="IndelSummary" />
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189 <option value="MendelianViolationEvaluator" />
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190 <option value="MultiallelicSummary" />
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191 <option value="PrintMissingComp" />
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192 <option value="ThetaVariantEvaluator" />
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193 <option value="TiTvVariantEvaluator" />
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194 <option value="ValidationReport" />
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195 <option value="VariantSummary" />
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196 </param>
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197 <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" />
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198
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199 <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &lt;numSamples&gt;"/>
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200 <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &lt;minPhaseQuality&gt;"/>
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201 <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &lt;mendelianViolationQualThreshold&gt;"/>
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202 <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &lt;ancestralAlignments&gt;" />
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203 <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &lt;knownCNVs&gt;" />
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204 <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &lt;stratIntervals&gt;" />
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205 </expand>
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206
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207 </inputs>
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208 <outputs>
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209 <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" />
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210 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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211 </outputs>
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212 <tests>
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213 <test>
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214 <param name="reference_source_selector" value="history" />
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215 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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216 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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217 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
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218 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
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219 <param name="dbsnp_rod_name" value="dbsnp" />
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220 <param name="dbsnp_known_names" value="True"/>
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221 <param name="comp_rod_bind" value="0" />
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222 <param name="gatk_param_type_selector" value="basic" />
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223 <param name="analysis_param_type_selector" value="basic" />
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224 <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" />
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225 <output name="output_log" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains" compare="contains" />
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226 </test>
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227 </tests>
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228 <help>
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229 **What it does**
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230
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231 General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
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232
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233 For more information on using the VariantEval module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_varianteval_VariantEval.html>`_.
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234
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235 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.
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236
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237 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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238
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239 ------
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240
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241 **Inputs**
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242
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243 GenomeAnalysisTK: VariantEval accepts variant files as input.
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244
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245
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246 **Outputs**
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247
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248 The output is a table of variant evaluation.
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249
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250
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251 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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252
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253 -------
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254
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255 **Settings**::
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256
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257 out An output file presented to the walker. Will overwrite contents if file exists.
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258 list List the available eval modules and exit
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259 select_exps One or more stratifications to use when evaluating the data
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260 select_names Names to use for the list of stratifications (must be a 1-to-1 mapping)
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261 sample Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context
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262 known_names Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets
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263 stratificationModule One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)
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264 doNotUseAllStandardStratifications Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)
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265 onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in
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266 evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)
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267 doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option)
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268 numSamples Number of samples (used if no samples are available in the VCF file
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269 minPhaseQuality Minimum phasing quality
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270 mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation
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271 ancestralAlignments Fasta file with ancestral alleles
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272
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273 @CITATION_SECTION@
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274 </help>
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275 <expand macro="citations" />
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276 </tool>
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