Mercurial > repos > devteam > table_recalibration
diff variant_recalibrator.xml @ 1:94379e2fc3e4 draft default tip
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| author | devteam |
|---|---|
| date | Mon, 14 Apr 2014 08:46:59 -0400 |
| parents | dfd818e0c4ac |
| children |
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--- a/variant_recalibrator.xml Tue Apr 01 09:12:12 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,431 +0,0 @@ -<tool id="gatk_variant_recalibrator" name="Variant Recalibrator" version="0.0.4"> - <description></description> - <requirements> - <requirement type="package" version="1.4">gatk</requirement> - </requirements> - <macros> - <import>gatk_macros.xml</import> - </macros> - <command interpreter="python">gatk_wrapper.py - --max_jvm_heap_fraction "1" - --stdout "${output_log}" - #for $var_count, $variant in enumerate( $reference_source.variants ): - -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" - #end for - -p 'java - -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" - -T "VariantRecalibrator" - --num_threads \${GALAXY_SLOTS:-4} - -et "NO_ET" ##ET no phone home - ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout - #if $reference_source.reference_source_selector != "history": - -R "${reference_source.ref_file.fields.path}" - #end if - --recal_file "${output_recal}" - --tranches_file "${output_tranches}" - --rscript_file "${output_rscript}" - ' - - #set $rod_binding_names = dict() - #for $rod_binding in $rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp': - #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector - #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known": - -d "--resource:${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[$rod_bind_name]}" - #else: - -d "--resource:${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]}" - #end if - #end for - - #include source=$standard_gatk_options# - - ##start analysis specific options - -p ' - #if str( $annotations ) != "None": - #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ): - --use_annotation "${annotation}" - #end for - #end if - #for $additional_annotation in $additional_annotations: - --use_annotation "${additional_annotation.additional_annotation_name}" - #end for - --mode "${mode}" - ' - - #if $analysis_param_type.analysis_param_type_selector == "advanced": - -p ' - --maxGaussians "${analysis_param_type.max_gaussians}" - --maxIterations "${analysis_param_type.max_iterations}" - --numKMeans "${analysis_param_type.num_k_means}" - --stdThreshold "${analysis_param_type.std_threshold}" - --qualThreshold "${analysis_param_type.qual_threshold}" - --shrinkage "${analysis_param_type.shrinkage}" - --dirichlet "${analysis_param_type.dirichlet}" - --priorCounts "${analysis_param_type.prior_counts}" - #if str( $analysis_param_type.bad_variant_selector.bad_variant_selector_type ) == 'percent': - --percentBadVariants "${analysis_param_type.bad_variant_selector.percent_bad_variants}" - #else: - --minNumBadVariants "${analysis_param_type.bad_variant_selector.min_num_bad_variants}" - #end if - --target_titv "${analysis_param_type.target_titv}" - #for $tranche in [ $tranche.strip() for $tranche in str( $analysis_param_type.ts_tranche ).split( ',' ) if $tranche.strip() ] - --TStranche "${tranche}" - #end for - #for $ignore_filter in $analysis_param_type.ignore_filters: - #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) - #if $ignore_filter_name == "custom": - #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) - #end if - --ignore_filter "${ignore_filter_name}" - #end for - --ts_filter_level "${analysis_param_type.ts_filter_level}" - ' - #end if - - - && - mv "${output_rscript}.pdf" "${output_tranches_pdf}" - - </command> - <inputs> - <conditional name="reference_source"> - <expand macro="reference_source_selector_param" /> - <when value="cached"> - <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> - <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> - </repeat> - <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> - <options from_data_table="gatk_picard_indexes"> - <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> - </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> - </when> - <when value="history"> <!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> - <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> - </repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> - </when> - </conditional> - - <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &lt;resource&gt;"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="variant">Variants</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="hapmap">HapMap</option> - <option value="omni">OMNI</option> - <option value="mask">Mask</option> - <option value="custom">Custom</option> - <option value="comp">Comp</option> - </param> - <when value="variant"> - <param name="input_rod" type="data" format="vcf" label="Variant ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="comp"> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="mask"> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="dbsnp"> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="snps"> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="hapmap"> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="omni"> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf" label="ROD file" /> - <conditional name="rod_training_type"> - <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> - <option value="is_training_truth_known">Set training/truth/known sites</option> - <option value="not_training_truth_known" selected="True">Don't Set options</option> - </param> - <when value="not_training_truth_known"> - <!-- do nothing here --> - </when> - <when value="is_training_truth_known"> - <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> - <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> - <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> - <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> - <param name="prior" type="float" label="prior probability of being true" value="12.0"/> - </when> - </conditional> - </when> - </conditional> - </repeat> - - <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &lt;use_annotation&gt;"> - <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> - <options from_data_table="gatk_annotations"> - <filter type="multiple_splitter" column="tools_valid_for" separator=","/> - <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/> - </options> - </param> - - <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &lt;use_annotation&gt;"> - <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> - </repeat> - - <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"> - <option value="SNP" selected="True">SNP</option> - <option value="INDEL">INDEL</option> - <option value="BOTH">BOTH</option> - </param> - - <expand macro="gatk_param_type_conditional" /> - - <expand macro="analysis_type_conditional"> - <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians &lt;maxGaussians&gt;"/> - <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations &lt;maxIterations&gt;"/> - <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="30" help="-nKM,--numKMeans &lt;numKMeans&gt;"/> - <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="8.0" help="-std,--stdThreshold &lt;stdThreshold&gt;"/> - <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0" help="-qual,--qualThreshold &lt;qualThreshold&gt;"/> - <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage &lt;shrinkage&gt;"/> - <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet &lt;dirichlet&gt;"/> - <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;"/> - <conditional name="bad_variant_selector"> - <param name="bad_variant_selector_type" type="select" label="How to specify bad variants"> - <option value="percent" selected="True">Percent</option> - <option value="min_num">Number</option> - </param> - <when value="percent"> - <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03" help="-percentBad,--percentBadVariants &lt;percentBadVariants&gt;"/> - </when> - <when value="min_num"> - <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000" help="-minNumBad,--minNumBadVariants &lt;minNumBadVariants&gt;"/> - </when> - </conditional> - <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;"/> - <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;"/> - <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"> - <conditional name="ignore_filter_type"> - <param name="ignore_filter_type_selector" type="select" label="Filter Type"> - <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> - <option value="LowQual" >LowQual</option> - <option value="custom" selected="True">Other</option> - </param> - <when value="custom"> - <param name="filter_name" type="text" value="" label="Filter name"/> - </when> - <when value="HARD_TO_VALIDATE" /> - <when value="LowQual" /> - </conditional> - </repeat> - <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &lt;ts_filter_level&gt;"/> - </expand> - </inputs> - <outputs> - <data format="gatk_recal" name="output_recal" label="${tool.name} on ${on_string} (Recalibration File)" /> - <data format="gatk_tranche" name="output_tranches" label="${tool.name} on ${on_string} (Tranches File)" /> - <data format="txt" name="output_rscript" label="${tool.name} on ${on_string} (RScript File)" /> - <data format="pdf" name="output_tranches_pdf" label="${tool.name} on ${on_string} (PDF File)" /> - <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> - </outputs> - <tests> - <!-- ADD TESTS --> - </tests> - <help> -**What it does** - -Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score - -For more information on using the VariantRecalibrator module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration>`_. - -To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_. - -If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. - ------- - -**Inputs** - -GenomeAnalysisTK: VariantRecalibrator accepts a variant input file. - - -**Outputs** - -The output is in VCF format. - - -Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. - -------- - -**Settings**:: - - - tranches_file The output tranches file used by ApplyRecalibration - use_annotation The names of the annotations which should used for calculations - 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) - maxGaussians The maximum number of Gaussians to try during variational Bayes algorithm - maxIterations The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected. - numKMeans The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model. - 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. - qualThreshold If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model. - shrinkage The shrinkage parameter in variational Bayes algorithm. - dirichlet The dirichlet parameter in variational Bayes algorithm. - priorCounts The number of prior counts to use in variational Bayes algorithm. - percentBadVariants What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent. - minNumBadVariants The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary. - recal_file The output recal file used by ApplyRecalibration - 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! - 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) - ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file - 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 - rscript_file The output rscript file generated by the VQSR to aid in visualization of the input data and learned model - path_to_resources Path to resources folder holding the Sting R scripts. - ts_filter_level The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots - -@CITATION_SECTION@ - </help> -</tool>