Mercurial > repos > iuc > gatk2
view variant_filtration.xml @ 1:f760c0de8e3a draft
Uploaded
author | bgruening |
---|---|
date | Mon, 02 Dec 2013 10:36:02 -0500 |
parents | 340633249b3d |
children | 8bcc13094767 |
line wrap: on
line source
<tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.7"> <description>on VCF files</description> <expand macro="requirements" /> <macros> <import>gatk2_macros.xml</import> </macros> <command interpreter="python"> #from binascii import hexlify gatk2_wrapper.py --stdout "${output_log}" -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p ' @JAR_PATH@ -T "VariantFiltration" \$GATK2_SITE_OPTIONS @THREADS@ -o "${output_vcf}" #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if ' #for $variant_filter in $variant_filters: #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) ) -o '${ hexlify( $variant_filter ) }' #end for #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}" -p ' --maskExtension "${mask_rod_bind_type.mask_extension}" --maskName "${mask_rod_bind_type.mask_rod_name}" ' #end if #include source=$standard_gatk_options# ##start analysis specific options #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp": -p ' --clusterSize "${cluster_snp_type.cluster_size}" --clusterWindowSize "${cluster_snp_type.cluster_window_size}" ' #end if -p '${missing_values_in_expressions_should_evaluate_as_failing}' </command> <inputs> <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk2_picard_indexes"> <filter type="data_meta" key="dbkey" ref="input_variant" 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!!!! --> <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional> <repeat name="variant_filters" title="Variant Filters"> <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &lt;filterExpression&gt;)"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"/> </sanitizer> </param> <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &lt;filterName&gt;"/> <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &lt;genotypeFilterExpression&gt; and -G_filterName,--genotypeFilterName &lt;genotypeFilterName&gt; for filter type" /> </repeat> <conditional name="mask_rod_bind_type"> <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> <option value="set_mask" selected="True">Set maskP</option> <option value="exclude_mask">Don't set mask</option> </param> <when value="exclude_mask"> <!-- Do nothing here --> </when> <when value="set_mask"> <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &lt;mask&gt;" /> <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/> <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/> </when> </conditional> <expand macro="gatk_param_type_conditional" /> <conditional name="cluster_snp_type"> <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs"> <option value="cluster_snp">Cluster SNPs</option> <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option> </param> <when value="do_not_cluster_snp"> <!-- Do nothing here --> </when> <when value="cluster_snp"> <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &lt;clusterSize&gt;"/> <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &lt;clusterWindowSize&gt;"/> </when> </conditional> <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" /> </inputs> <outputs> <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> </outputs> <tests> <test> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="phiX.fasta" ftype="fasta" /> <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> <param name="filter_expression" value="MQ < 37.74 || MQ0 > 50" /> <param name="filter_name" value="Galaxy_filter" /> <param name="is_genotype_filter" /> <param name="mask_rod_bind_type_selector" value="set_mask" /> <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> <param name="mask_rod_name" value="." /> <param name="mask_extension" value="0" /> <param name="gatk_param_type_selector" value="basic" /> <param name="cluster_snp_type_selector" value="do_not_cluster_snp" /> <param name="missing_values_in_expressions_should_evaluate_as_failing" /> <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" /> </test> </tests> <help> **What it does** Filters variant calls using a number of user-selectable, parameterizable criteria. For more information on using the VariantFiltration module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_filters_VariantFiltration.html>`_. To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. ------ **Inputs** GenomeAnalysisTK: VariantFiltration accepts a VCF input file. **Outputs** The output is in VCF format. Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. ------- **Settings**:: filterExpression One or more expression used with INFO fields to filter (see wiki docs for more info) filterName Names to use for the list of filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered genotypeFilterExpression One or more expression used with FORMAT (sample/genotype-level) fields to filter (see wiki docs for more info) genotypeFilterName Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered clusterSize The number of SNPs which make up a cluster (see also --clusterWindowSize); [default:3] clusterWindowSize The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1); [default:0] maskName The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask'] missingValuesInExpressionsShouldEvaluateAsFailing When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)? @CITATION_SECTION@ </help> </tool>