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comparison variant_eval.xml @ 4:f244b8209eb8 draft

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bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 8bcc13094767
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
1 <tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.7"> 1 <tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0">
2 <description></description> 2 <description></description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>gatk2_macros.xml</import> 5 <import>gatk2_macros.xml</import>
6 </macros> 6 </macros>
77 #if str( $analysis_param_type.num_samples ) != "0": 77 #if str( $analysis_param_type.num_samples ) != "0":
78 --numSamples "${analysis_param_type.num_samples}" 78 --numSamples "${analysis_param_type.num_samples}"
79 #end if 79 #end if
80 80
81 --minPhaseQuality "${analysis_param_type.min_phase_quality}" 81 --minPhaseQuality "${analysis_param_type.min_phase_quality}"
82
83 #if str( $analysis_param_type.family ):
84 --family_structure "${analysis_param_type.family}"
85 #end if
86 82
87 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" 83 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
88 84
89 #if str( $analysis_param_type.ancestral_alignments ) != "None": 85 #if str( $analysis_param_type.ancestral_alignments ) != "None":
90 --ancestralAlignments "${analysis_param_type.ancestral_alignments}" 86 --ancestralAlignments "${analysis_param_type.ancestral_alignments}"
163 <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;"> 159 <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;">
164 <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"/> 160 <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"/>
165 </repeat> 161 </repeat>
166 162
167 <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" > 163 <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" >
168 <!-- do these need individual options also? gatk wiki has little info --> 164 <option value="AlleleCount" />
169 <option value="AlleleFrequency" /> 165 <option value="AlleleFrequency" />
170 <option value="AlleleCount" />
171 <option value="CompRod" /> 166 <option value="CompRod" />
172 <option value="Contig" /> 167 <option value="Contig" />
173 <option value="CpG" /> 168 <option value="CpG" />
174 <option value="Degeneracy" /> 169 <option value="Degeneracy" />
175 <option value="EvalRod" /> 170 <option value="EvalRod" />
176 <option value="Filter" /> 171 <option value="Filter" />
177 <option value="FunctionalClass" /> 172 <option value="FunctionalClass" />
173 <option value="IndelSize" />
174 <option value="IntervalStratification" />
178 <option value="JexlExpression" /> 175 <option value="JexlExpression" />
176 <option value="Novelty" />
177 <option value="OneBPIndel" />
179 <option value="Sample" /> 178 <option value="Sample" />
180 <option value="IntervalStratification" /> 179 <option value="SnpEffPositionModifier" />
180 <option value="TandemRepeat" />
181 <option value="VariantType" />
181 </param> 182 </param>
182 <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" /> 183 <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" />
183 184
184 <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType"> 185 <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
185 <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/> 186 <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
186 </repeat> 187 </repeat>
187 188
188 <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" > 189 <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" >
189 <!-- do these need individual options also? gatk wiki has little info -->
190 <option value="ACTransitionTable" />
191 <option value="AlleleFrequencyComparison" />
192 <option value="AminoAcidTransition" />
193 <option value="CompOverlap" /> 190 <option value="CompOverlap" />
194 <option value="CountVariants" /> 191 <option value="CountVariants" />
195 <option value="GenotypeConcordance" /> 192 <option value="IndelLengthHistogram" />
196 <option value="GenotypePhasingEvaluator" /> 193 <option value="IndelSummary" />
197 <option value="IndelMetricsByAC" />
198 <option value="IndelStatistics" />
199 <option value="MendelianViolationEvaluator" /> 194 <option value="MendelianViolationEvaluator" />
195 <option value="MultiallelicSummary" />
200 <option value="PrintMissingComp" /> 196 <option value="PrintMissingComp" />
201 <option value="PrivatePermutations" />
202 <option value="SimpleMetricsByAC" />
203 <option value="ThetaVariantEvaluator" /> 197 <option value="ThetaVariantEvaluator" />
204 <option value="TiTvVariantEvaluator" /> 198 <option value="TiTvVariantEvaluator" />
205 <option value="VariantQualityScore" /> 199 <option value="ValidationReport" />
200 <option value="VariantSummary" />
206 </param> 201 </param>
207 <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" /> 202 <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" />
208 203
209 <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 &amp;lt;numSamples&amp;gt;"/> 204 <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 &amp;lt;numSamples&amp;gt;"/>
210 <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/> 205 <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/>
211 <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined" help="--family_structure"/>
212 <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 &amp;lt;mendelianViolationQualThreshold&amp;gt;"/> 206 <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 &amp;lt;mendelianViolationQualThreshold&amp;gt;"/>
213 <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" /> 207 <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" />
214 <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 &amp;lt;knownCNVs&amp;gt;" /> 208 <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 &amp;lt;knownCNVs&amp;gt;" />
215 <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 &amp;lt;stratIntervals&amp;gt;" /> 209 <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 &amp;lt;stratIntervals&amp;gt;" />
216 210
278 onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in 272 onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in
279 evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified) 273 evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)
280 doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option) 274 doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option)
281 numSamples Number of samples (used if no samples are available in the VCF file 275 numSamples Number of samples (used if no samples are available in the VCF file
282 minPhaseQuality Minimum phasing quality 276 minPhaseQuality Minimum phasing quality
283 family_structure If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined
284 mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation 277 mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation
285 ancestralAlignments Fasta file with ancestral alleles 278 ancestralAlignments Fasta file with ancestral alleles
286 279
287 @CITATION_SECTION@ 280 @CITATION_SECTION@
288 </help> 281 </help>
282 <expand macro="citations" />
289 </tool> 283 </tool>