Mercurial > repos > iuc > gatk2
annotate variant_recalibrator.xml @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 05:38:15 -0400 |
| parents | 84584664264c |
| children |
| rev | line source |
|---|---|
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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changeset
|
1 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.1"> |
| 0 | 2 <description></description> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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changeset
|
3 <macros> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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4 <import>gatk2_macros.xml</import> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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|
5 </macros> |
| 4 | 6 <expand macro="requirements"> |
| 5 | 7 <requirement type="package" version="0.9.3">ggplot2</requirement> |
| 4 | 8 </expand> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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9 <expand macro="version_command" /> |
| 0 | 10 <command interpreter="python"> |
| 11 gatk2_wrapper.py | |
| 12 --stdout "${output_log}" | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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13 #for $var_count, $variant in enumerate( $reference_source.input_variants ): |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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14 -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}" |
| 0 | 15 #end for |
| 16 -p ' | |
| 17 @JAR_PATH@ | |
| 18 -T "VariantRecalibrator" | |
| 19 \$GATK2_SITE_OPTIONS | |
| 20 | |
| 21 @THREADS@ | |
| 22 | |
| 23 #if $reference_source.reference_source_selector != "history": | |
| 24 -R "${reference_source.ref_file.fields.path}" | |
| 25 #end if | |
| 26 --recal_file "${output_recal}" | |
| 27 --tranches_file "${output_tranches}" | |
| 28 --rscript_file "${output_rscript}" | |
| 29 ' | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
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30 |
| 0 | 31 #set $rod_binding_names = dict() |
| 32 #for $rod_binding in $rod_bind: | |
| 33 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': | |
| 34 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name | |
| 35 #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp': | |
| 36 #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
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37 #else |
| 0 | 38 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector |
| 39 #end if | |
| 40 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 | |
| 41 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known": | |
| 42 -d "--resource:${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[$rod_bind_name]}" | |
| 43 #else: | |
| 44 -d "--resource:${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]}" | |
| 45 #end if | |
| 46 #end for | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
|
47 |
| 0 | 48 #include source=$standard_gatk_options# |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
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49 |
| 0 | 50 ##start analysis specific options |
| 51 -p ' | |
| 52 #if str( $annotations ) != "None": | |
| 53 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ): | |
| 54 --use_annotation "${annotation}" | |
| 55 #end for | |
| 56 #end if | |
| 57 #for $additional_annotation in $additional_annotations: | |
| 58 --use_annotation "${additional_annotation.additional_annotation_name}" | |
| 59 #end for | |
| 60 --mode "${mode}" | |
| 61 ' | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
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62 |
| 0 | 63 #if $analysis_param_type.analysis_param_type_selector == "advanced": |
| 64 -p ' | |
| 65 --maxGaussians "${analysis_param_type.max_gaussians}" | |
| 66 --maxIterations "${analysis_param_type.max_iterations}" | |
| 67 --numKMeans "${analysis_param_type.num_k_means}" | |
| 68 --stdThreshold "${analysis_param_type.std_threshold}" | |
| 69 --shrinkage "${analysis_param_type.shrinkage}" | |
| 70 --dirichlet "${analysis_param_type.dirichlet}" | |
| 71 --priorCounts "${analysis_param_type.prior_counts}" | |
| 4 | 72 |
| 73 --minNumBadVariants "${analysis_param_type.min_num_bad_variants}" | |
| 74 | |
| 0 | 75 --target_titv "${analysis_param_type.target_titv}" |
| 76 #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ] | |
| 77 --TStranche "${tranche}" | |
| 78 #end for | |
| 79 #for $ignore_filter in $analysis_param_type.ignore_filters: | |
| 80 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) | |
| 81 #if $ignore_filter_name == "custom": | |
| 82 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) | |
| 83 #end if | |
| 84 --ignore_filter "${ignore_filter_name}" | |
| 85 #end for | |
| 86 ' | |
| 87 #end if | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
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88 |
| 0 | 89 && |
| 90 mv "${output_rscript}.pdf" "${output_tranches_pdf}" | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
|
91 |
| 0 | 92 </command> |
| 93 <inputs> | |
| 94 <conditional name="reference_source"> | |
| 95 <expand macro="reference_source_selector_param" /> | |
| 96 <when value="cached"> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
|
97 <expand macro="input_variants" /> |
| 0 | 98 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> |
| 4 | 99 <options from_data_table="gatk2_picard_indexes"> |
| 0 | 100 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> |
| 101 </options> | |
| 102 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 103 </param> | |
| 104 </when> | |
| 105 <when value="history"> <!-- FIX ME!!!! --> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
|
106 <expand macro="input_variants" /> |
| 0 | 107 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> |
| 108 </when> | |
| 109 </conditional> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
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110 |
| 4 | 111 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &lt;resource&gt;" min="2"> |
| 0 | 112 <conditional name="rod_bind_type"> |
| 113 <param name="rod_bind_type_selector" type="select" label="Binding Type"> | |
| 114 <option value="dbsnp" selected="True">dbSNP</option> | |
| 115 <option value="variant">Variants</option> | |
| 116 <option value="snps">SNPs</option> | |
| 117 <option value="indels">INDELs</option> | |
| 118 <option value="hapmap">HapMap</option> | |
| 119 <option value="omni">OMNI</option> | |
| 120 <option value="mask">Mask</option> | |
| 121 <option value="custom">Custom</option> | |
| 122 <option value="comp">Comp</option> | |
| 123 </param> | |
| 124 <when value="variant"> | |
| 125 <param name="input_rod" type="data" format="vcf" label="Variant ROD file" /> | |
| 126 <conditional name="rod_training_type"> | |
| 127 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 128 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 129 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 130 </param> | |
| 131 <when value="not_training_truth_known"> | |
| 132 <!-- do nothing here --> | |
| 133 </when> | |
| 134 <when value="is_training_truth_known"> | |
| 135 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 136 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 137 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 138 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 139 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 140 </when> | |
| 141 </conditional> | |
| 142 </when> | |
| 143 <when value="comp"> | |
| 144 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 145 <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/> | |
| 146 <conditional name="rod_training_type"> | |
| 147 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 148 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 149 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 150 </param> | |
| 151 <when value="not_training_truth_known"> | |
| 152 <!-- do nothing here --> | |
| 153 </when> | |
| 154 <when value="is_training_truth_known"> | |
| 155 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 156 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 157 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 158 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 159 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 160 </when> | |
| 161 </conditional> | |
| 162 </when> | |
| 163 <when value="mask"> | |
| 164 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 165 <conditional name="rod_training_type"> | |
| 166 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 167 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 168 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 169 </param> | |
| 170 <when value="not_training_truth_known"> | |
| 171 <!-- do nothing here --> | |
| 172 </when> | |
| 173 <when value="is_training_truth_known"> | |
| 174 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 175 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 176 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 177 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 178 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 179 </when> | |
| 180 </conditional> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
|
181 </when> |
| 0 | 182 <when value="dbsnp"> |
| 183 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 184 <conditional name="rod_training_type"> | |
| 185 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 186 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 187 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 188 </param> | |
| 189 <when value="not_training_truth_known"> | |
| 190 <!-- do nothing here --> | |
| 191 </when> | |
| 192 <when value="is_training_truth_known"> | |
| 193 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 194 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 195 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 196 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 197 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 198 </when> | |
| 199 </conditional> | |
| 200 </when> | |
| 201 <when value="snps"> | |
| 202 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 203 <conditional name="rod_training_type"> | |
| 204 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 205 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 206 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 207 </param> | |
| 208 <when value="not_training_truth_known"> | |
| 209 <!-- do nothing here --> | |
| 210 </when> | |
| 211 <when value="is_training_truth_known"> | |
| 212 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 213 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 214 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 215 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 216 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 217 </when> | |
| 218 </conditional> | |
| 219 </when> | |
| 220 <when value="hapmap"> | |
| 221 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 222 <conditional name="rod_training_type"> | |
| 223 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 224 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 225 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 226 </param> | |
| 227 <when value="not_training_truth_known"> | |
| 228 <!-- do nothing here --> | |
| 229 </when> | |
| 230 <when value="is_training_truth_known"> | |
| 231 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 232 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 233 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 234 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 235 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 236 </when> | |
| 237 </conditional> | |
| 238 </when> | |
| 239 <when value="omni"> | |
| 240 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 241 <conditional name="rod_training_type"> | |
| 242 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 243 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 244 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 245 </param> | |
| 246 <when value="not_training_truth_known"> | |
| 247 <!-- do nothing here --> | |
| 248 </when> | |
| 249 <when value="is_training_truth_known"> | |
| 250 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 251 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 252 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 253 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 254 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 255 </when> | |
| 256 </conditional> | |
| 257 </when> | |
| 258 <when value="indels"> | |
| 259 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 260 <conditional name="rod_training_type"> | |
| 261 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 262 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 263 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 264 </param> | |
| 265 <when value="not_training_truth_known"> | |
| 266 <!-- do nothing here --> | |
| 267 </when> | |
| 268 <when value="is_training_truth_known"> | |
| 269 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 270 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 271 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 272 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 273 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 274 </when> | |
| 275 </conditional> | |
| 276 </when> | |
| 277 <when value="custom"> | |
| 278 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> | |
| 279 <param name="input_rod" type="data" format="vcf" label="ROD file" /> | |
| 280 <conditional name="rod_training_type"> | |
| 281 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> | |
| 282 <option value="is_training_truth_known">Set training/truth/known sites</option> | |
| 283 <option value="not_training_truth_known" selected="True">Don't Set options</option> | |
| 284 </param> | |
| 285 <when value="not_training_truth_known"> | |
| 286 <!-- do nothing here --> | |
| 287 </when> | |
| 288 <when value="is_training_truth_known"> | |
| 289 <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> | |
| 290 <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> | |
| 291 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> | |
| 292 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> | |
| 293 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> | |
| 294 </when> | |
| 295 </conditional> | |
| 296 </when> | |
| 297 </conditional> | |
| 298 </repeat> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
|
299 |
| 0 | 300 <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &lt;use_annotation&gt;"> |
| 301 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | |
| 302 <options from_data_table="gatk2_annotations"> | |
| 303 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | |
| 304 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/> | |
| 305 </options> | |
| 306 </param> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
5
diff
changeset
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307 |
| 0 | 308 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &lt;use_annotation&gt;"> |
| 309 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> | |
| 310 </repeat> | |
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| 0 | 312 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"> |
| 313 <option value="SNP" selected="True">SNP</option> | |
| 314 <option value="INDEL">INDEL</option> | |
| 315 <option value="BOTH">BOTH</option> | |
| 316 </param> | |
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| 0 | 318 <expand macro="gatk_param_type_conditional" /> |
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| 0 | 320 <expand macro="analysis_type_conditional"> |
| 4 | 321 <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;"/> |
| 322 <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;"/> | |
| 323 <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;"/> | |
| 324 <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;"/> | |
| 0 | 325 <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &lt;shrinkage&gt;"/> |
| 326 <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &lt;dirichlet&gt;"/> | |
| 327 <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;"/> | |
| 4 | 328 <!--<param name="trustAllPolymorphic" type="boolean" label="trustAllPolymorphic" truevalue="-/-trustAllPolymorphic=true" falsevalue="-/-trustAllPolymorphic=false" |
| 329 help="Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation. -trustAllPolymorphic" />--> | |
| 330 <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;"/> | |
| 0 | 331 <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;"/> |
| 332 <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;"/> | |
| 333 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"> | |
| 334 <conditional name="ignore_filter_type"> | |
| 335 <param name="ignore_filter_type_selector" type="select" label="Filter Type"> | |
| 336 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> | |
| 337 <option value="LowQual" >LowQual</option> | |
| 338 <option value="custom" selected="True">Other</option> | |
| 339 </param> | |
| 340 <when value="custom"> | |
| 341 <param name="filter_name" type="text" value="" label="Filter name"/> | |
| 342 </when> | |
| 343 <when value="HARD_TO_VALIDATE" /> | |
| 344 <when value="LowQual" /> | |
| 345 </conditional> | |
| 346 </repeat> | |
| 347 </expand> | |
| 348 </inputs> | |
| 349 <outputs> | |
| 350 <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" /> | |
| 351 <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" /> | |
| 352 <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" /> | |
| 353 <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" /> | |
| 354 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 355 </outputs> | |
| 356 <tests> | |
| 357 <!-- ADD TESTS --> | |
| 358 </tests> | |
| 359 <help> | |
| 360 **What it does** | |
| 361 | |
| 362 Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score | |
| 363 | |
| 364 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>`_. | |
| 365 | |
| 366 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 367 | |
| 368 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 369 | |
| 370 ------ | |
| 371 | |
| 372 **Inputs** | |
| 373 | |
| 374 GenomeAnalysisTK: VariantRecalibrator accepts a variant input file. | |
| 375 | |
| 376 | |
| 377 **Outputs** | |
| 378 | |
| 379 The output is in VCF format. | |
| 380 | |
| 381 | |
| 382 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 383 | |
| 384 ------- | |
| 385 | |
| 386 **Settings**:: | |
| 387 | |
| 388 | |
| 389 tranches_file The output tranches file used by ApplyRecalibration | |
| 390 use_annotation The names of the annotations which should used for calculations | |
| 391 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) | |
| 392 maxGaussians The maximum number of Gaussians to try during variational Bayes algorithm | |
| 393 maxIterations The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected. | |
| 394 numKMeans The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model. | |
| 395 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. | |
| 396 shrinkage The shrinkage parameter in variational Bayes algorithm. | |
| 397 dirichlet The dirichlet parameter in variational Bayes algorithm. | |
| 398 priorCounts The number of prior counts to use in variational Bayes algorithm. | |
| 4 | 399 minNumBadVariants The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. |
| 0 | 400 recal_file The output recal file used by ApplyRecalibration |
| 401 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! | |
| 402 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) | |
| 403 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file | |
| 404 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 | |
| 405 rscript_file The output rscript file generated by the VQSR to aid in visualization of the input data and learned model | |
| 406 path_to_resources Path to resources folder holding the Sting R scripts. | |
| 407 | |
| 408 @CITATION_SECTION@ | |
| 409 </help> | |
| 4 | 410 <expand macro="citations" /> |
| 0 | 411 </tool> |