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1 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.0">
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2 <description></description>
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3 <expand macro="requirements">
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4 <requirement type="package" version="0.9.3">ggplot</requirement>
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5 </expand>
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6 <macros>
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7 <import>gatk2_macros.xml</import>
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8 </macros>
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9 <command interpreter="python">
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10 gatk2_wrapper.py
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11 --stdout "${output_log}"
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12 #for $var_count, $variant in enumerate( $reference_source.variants ):
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13 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
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14 #end for
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15 -p '
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16 @JAR_PATH@
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17 -T "VariantRecalibrator"
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18 \$GATK2_SITE_OPTIONS
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19
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20 @THREADS@
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21
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22 #if $reference_source.reference_source_selector != "history":
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23 -R "${reference_source.ref_file.fields.path}"
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24 #end if
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25 --recal_file "${output_recal}"
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26 --tranches_file "${output_tranches}"
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27 --rscript_file "${output_rscript}"
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28 '
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29
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30 #set $rod_binding_names = dict()
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31 #for $rod_binding in $rod_bind:
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32 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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33 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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34 #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
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35 #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
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36 #else
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37 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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38 #end if
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39 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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40 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
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41 -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
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42 #else:
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43 -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
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44 #end if
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45 #end for
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46
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47 #include source=$standard_gatk_options#
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48
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49 ##start analysis specific options
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50 -p '
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51 #if str( $annotations ) != "None":
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52 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
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53 --use_annotation "${annotation}"
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54 #end for
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55 #end if
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56 #for $additional_annotation in $additional_annotations:
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57 --use_annotation "${additional_annotation.additional_annotation_name}"
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58 #end for
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59 --mode "${mode}"
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60 '
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61
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62 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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63 -p '
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64 --maxGaussians "${analysis_param_type.max_gaussians}"
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65 --maxIterations "${analysis_param_type.max_iterations}"
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66 --numKMeans "${analysis_param_type.num_k_means}"
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67 --stdThreshold "${analysis_param_type.std_threshold}"
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68 --shrinkage "${analysis_param_type.shrinkage}"
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69 --dirichlet "${analysis_param_type.dirichlet}"
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70 --priorCounts "${analysis_param_type.prior_counts}"
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71
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72 --minNumBadVariants "${analysis_param_type.min_num_bad_variants}"
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73
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74 --target_titv "${analysis_param_type.target_titv}"
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75 #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ]
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76 --TStranche "${tranche}"
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77 #end for
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78 #for $ignore_filter in $analysis_param_type.ignore_filters:
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79 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
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80 #if $ignore_filter_name == "custom":
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81 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
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82 #end if
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83 --ignore_filter "${ignore_filter_name}"
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84 #end for
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85 '
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86 #end if
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87
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88
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89 &&
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90 mv "${output_rscript}.pdf" "${output_tranches_pdf}"
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91
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92 </command>
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93 <inputs>
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94 <conditional name="reference_source">
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95 <expand macro="reference_source_selector_param" />
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96 <when value="cached">
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97 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;">
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98 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
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99 </repeat>
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100 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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101 <options from_data_table="gatk2_picard_indexes">
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102 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
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103 </options>
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104 <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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105 </param>
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106 </when>
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107 <when value="history"> <!-- FIX ME!!!! -->
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108 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;">
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109 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
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110 </repeat>
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111 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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112 </when>
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113 </conditional>
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114
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115 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &lt;resource&gt;" min="2">
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116 <conditional name="rod_bind_type">
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117 <param name="rod_bind_type_selector" type="select" label="Binding Type">
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118 <option value="dbsnp" selected="True">dbSNP</option>
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119 <option value="variant">Variants</option>
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120 <option value="snps">SNPs</option>
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121 <option value="indels">INDELs</option>
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122 <option value="hapmap">HapMap</option>
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123 <option value="omni">OMNI</option>
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124 <option value="mask">Mask</option>
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125 <option value="custom">Custom</option>
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126 <option value="comp">Comp</option>
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127 </param>
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128 <when value="variant">
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129 <param name="input_rod" type="data" format="vcf" label="Variant ROD file" />
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130 <conditional name="rod_training_type">
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131 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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132 <option value="is_training_truth_known">Set training/truth/known sites</option>
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133 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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134 </param>
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135 <when value="not_training_truth_known">
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136 <!-- do nothing here -->
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137 </when>
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138 <when value="is_training_truth_known">
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139 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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140 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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141 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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142 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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143 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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144 </when>
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145 </conditional>
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146 </when>
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147 <when value="comp">
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148 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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149 <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/>
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150 <conditional name="rod_training_type">
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151 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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152 <option value="is_training_truth_known">Set training/truth/known sites</option>
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153 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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154 </param>
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155 <when value="not_training_truth_known">
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156 <!-- do nothing here -->
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157 </when>
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158 <when value="is_training_truth_known">
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159 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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160 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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161 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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162 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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163 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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164 </when>
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165 </conditional>
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166 </when>
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167 <when value="mask">
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168 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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169 <conditional name="rod_training_type">
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170 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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171 <option value="is_training_truth_known">Set training/truth/known sites</option>
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172 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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173 </param>
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174 <when value="not_training_truth_known">
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175 <!-- do nothing here -->
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176 </when>
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177 <when value="is_training_truth_known">
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178 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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179 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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180 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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181 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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182 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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183 </when>
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184 </conditional>
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185 </when>
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186 <when value="dbsnp">
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187 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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188 <conditional name="rod_training_type">
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189 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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190 <option value="is_training_truth_known">Set training/truth/known sites</option>
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191 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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192 </param>
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193 <when value="not_training_truth_known">
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194 <!-- do nothing here -->
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195 </when>
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196 <when value="is_training_truth_known">
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197 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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198 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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199 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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200 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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201 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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202 </when>
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203 </conditional>
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204 </when>
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205 <when value="snps">
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206 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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207 <conditional name="rod_training_type">
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208 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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209 <option value="is_training_truth_known">Set training/truth/known sites</option>
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210 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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211 </param>
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212 <when value="not_training_truth_known">
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213 <!-- do nothing here -->
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214 </when>
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215 <when value="is_training_truth_known">
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216 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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217 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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218 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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219 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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220 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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221 </when>
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222 </conditional>
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223 </when>
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224 <when value="hapmap">
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225 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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226 <conditional name="rod_training_type">
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227 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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228 <option value="is_training_truth_known">Set training/truth/known sites</option>
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229 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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230 </param>
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231 <when value="not_training_truth_known">
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232 <!-- do nothing here -->
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233 </when>
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234 <when value="is_training_truth_known">
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235 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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236 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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237 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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238 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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239 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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240 </when>
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241 </conditional>
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242 </when>
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243 <when value="omni">
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244 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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245 <conditional name="rod_training_type">
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246 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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247 <option value="is_training_truth_known">Set training/truth/known sites</option>
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248 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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249 </param>
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250 <when value="not_training_truth_known">
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251 <!-- do nothing here -->
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252 </when>
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253 <when value="is_training_truth_known">
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254 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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255 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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256 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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257 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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258 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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259 </when>
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260 </conditional>
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261 </when>
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262 <when value="indels">
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263 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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264 <conditional name="rod_training_type">
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265 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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266 <option value="is_training_truth_known">Set training/truth/known sites</option>
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267 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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268 </param>
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269 <when value="not_training_truth_known">
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270 <!-- do nothing here -->
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271 </when>
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272 <when value="is_training_truth_known">
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273 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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274 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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275 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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276 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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277 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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278 </when>
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279 </conditional>
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280 </when>
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281 <when value="custom">
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282 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
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283 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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284 <conditional name="rod_training_type">
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285 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
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286 <option value="is_training_truth_known">Set training/truth/known sites</option>
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287 <option value="not_training_truth_known" selected="True">Don't Set options</option>
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288 </param>
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289 <when value="not_training_truth_known">
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290 <!-- do nothing here -->
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291 </when>
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292 <when value="is_training_truth_known">
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293 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/>
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294 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/>
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295 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
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296 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
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297 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
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298 </when>
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299 </conditional>
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300 </when>
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301 </conditional>
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302 </repeat>
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303
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304 <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &lt;use_annotation&gt;">
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305 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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306 <options from_data_table="gatk2_annotations">
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307 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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308 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
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309 </options>
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310 </param>
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311
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312 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &lt;use_annotation&gt;">
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313 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
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314 </repeat>
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315
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316 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;">
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317 <option value="SNP" selected="True">SNP</option>
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318 <option value="INDEL">INDEL</option>
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319 <option value="BOTH">BOTH</option>
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320 </param>
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321
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322 <expand macro="gatk_param_type_conditional" />
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323
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324 <expand macro="analysis_type_conditional">
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325 <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="8" help="-mG,--maxGaussians &lt;maxGaussians&gt;"/>
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326 <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="150" help="-mI,--maxIterations &lt;maxIterations&gt;"/>
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327 <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="100" help="-nKM,--numKMeans &lt;numKMeans&gt;"/>
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328 <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="10.0" help="-std,--stdThreshold &lt;stdThreshold&gt;"/>
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0
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329 <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &lt;shrinkage&gt;"/>
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330 <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &lt;dirichlet&gt;"/>
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331 <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0" help="-priorCounts,--priorCounts &lt;priorCounts&gt;"/>
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332 <!--<param name="trustAllPolymorphic" type="boolean" label="trustAllPolymorphic" truevalue="-/-trustAllPolymorphic=true" falsevalue="-/-trustAllPolymorphic=false"
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333 help="Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation. -trustAllPolymorphic" />-->
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334 <param name="min_num_bad_variants" type="integer" label="Minimum number of worst scoring variants to use when building the Gaussian mixture model of bad variants" value="1000" help="--minNumBadVariants &lt;minNumBadVariants&gt;"/>
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0
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335 <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15" help="-titv,--target_titv &lt;target_titv&gt;"/>
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336 <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0" help="-tranche,--TStranche &lt;TStranche&gt;"/>
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337 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;">
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338 <conditional name="ignore_filter_type">
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339 <param name="ignore_filter_type_selector" type="select" label="Filter Type">
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340 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
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341 <option value="LowQual" >LowQual</option>
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342 <option value="custom" selected="True">Other</option>
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343 </param>
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344 <when value="custom">
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345 <param name="filter_name" type="text" value="" label="Filter name"/>
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346 </when>
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347 <when value="HARD_TO_VALIDATE" />
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348 <when value="LowQual" />
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349 </conditional>
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350 </repeat>
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351 </expand>
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352 </inputs>
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353 <outputs>
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354 <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" />
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355 <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" />
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356 <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" />
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357 <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" />
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358 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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359 </outputs>
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360 <tests>
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361 <!-- ADD TESTS -->
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362 </tests>
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363 <help>
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364 **What it does**
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365
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366 Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score
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367
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368 For more information on using the VariantRecalibrator module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_VariantRecalibrator.html>`_.
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369
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370 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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371
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372 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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373
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374 ------
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375
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376 **Inputs**
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377
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378 GenomeAnalysisTK: VariantRecalibrator accepts a variant input file.
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379
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380
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381 **Outputs**
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382
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383 The output is in VCF format.
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384
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385
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386 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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387
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388 -------
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389
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390 **Settings**::
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391
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392
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393 tranches_file The output tranches file used by ApplyRecalibration
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394 use_annotation The names of the annotations which should used for calculations
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395 mode Recalibration mode to employ: 1.) SNP for recalibrating only snps (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both snps and indels simultaneously. (SNP|INDEL|BOTH)
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396 maxGaussians The maximum number of Gaussians to try during variational Bayes algorithm
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397 maxIterations The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.
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398 numKMeans The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.
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399 stdThreshold If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model.
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400 shrinkage The shrinkage parameter in variational Bayes algorithm.
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401 dirichlet The dirichlet parameter in variational Bayes algorithm.
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402 priorCounts The number of prior counts to use in variational Bayes algorithm.
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4
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403 minNumBadVariants The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants.
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0
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404 recal_file The output recal file used by ApplyRecalibration
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405 target_titv The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!
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406 TStranche The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)
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407 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
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408 path_to_Rscript The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript
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409 rscript_file The output rscript file generated by the VQSR to aid in visualization of the input data and learned model
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410 path_to_resources Path to resources folder holding the Sting R scripts.
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411
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412 @CITATION_SECTION@
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413 </help>
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4
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414 <expand macro="citations" />
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0
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415 </tool>
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