Mercurial > repos > devteam > variant_eval
diff variant_eval.xml @ 0:b3a0923b33ed draft default tip
Imported from capsule None
| author | devteam |
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| date | Tue, 01 Apr 2014 09:12:07 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_eval.xml Tue Apr 01 09:12:07 2014 -0400 @@ -0,0 +1,288 @@ +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.8"> + <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 + #from binascii import hexlify + --max_jvm_heap_fraction "1" + --stdout "${output_log}" + #for $var_count, $variant in enumerate( $reference_source.variants ): + -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" + #end for + -p 'java + -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" + -T "VariantEval" + --out "${output_report}" + --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 + ' + + #for $rod_binding in $comp_rod_bind: + -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}" + #if str( $rod_binding.comp_known_names ): + -p '--known_names "${rod_binding.comp_rod_name}"' + #end if + #end for + + #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': + -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}" + #if str( $dbsnp_rod_bind_type.dbsnp_known_names ): + -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"' + #end if + #end if + + #include source=$standard_gatk_options# + + + ##start analysis specific options + #if $analysis_param_type.analysis_param_type_selector == "advanced": + #for $stratification in $analysis_param_type.stratifications: + #set $select_string = "--select_exps '%s' --select_names '%s'" % ( str( $stratification.select_exps ), str( $stratification.select_name ) ) + -o '${ hexlify( $select_string ) }' + #end for + -p ' + + #for $sample in $analysis_param_type.samples: + --sample "${sample.sample}" + #end for + + #if str( $analysis_param_type.stratification_modules ) != "None": + #for $stratification_module in str( $analysis_param_type.stratification_modules).split( ',' ): + --stratificationModule "${stratification_module}" + #end for + #end if + + ${analysis_param_type.do_not_use_all_standard_stratifications} + + #for $variant_type in $analysis_param_type.only_variants_of_type: + --onlyVariantsOfType "${variant_type.variant_type}" + #end for + + #if str( $analysis_param_type.eval_modules ) != "None": + #for $eval_module in str( $analysis_param_type.eval_modules).split( ',' ): + --evalModule "${eval_module}" + #end for + #end if + + ${analysis_param_type.do_not_use_all_standard_modules} + + #if str( $analysis_param_type.num_samples ) != "0": + --numSamples "${analysis_param_type.num_samples}" + #end if + + --minPhaseQuality "${analysis_param_type.min_phase_quality}" + + #if str( $analysis_param_type.family ): + --family_structure "${analysis_param_type.family}" + #end if + + --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" + + #if str( $analysis_param_type.ancestral_alignments ) != "None": + --ancestralAlignments "${analysis_param_type.ancestral_alignments}" + #end if + ' + #if str( $analysis_param_type.known_cnvs ) != "None": + -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs" + #end if + + #if str( $analysis_param_type.strat_intervals ) != "None": + -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals" + #end if + #end if + </command> + <inputs> + + <conditional name="reference_source"> + <expand macro="reference_source_selector_param" /> + <when value="cached"> + <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> + <param name="input_variant" type="data" format="vcf" label="Input variant file" /> + </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="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!!!! --> + <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> + <param name="input_variant" type="data" format="vcf" label="Input variant file" /> + </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="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &lt;comp&gt;"> + <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> + <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/> + <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names &lt;known_names&gt;"/> + </repeat> + + <conditional name="dbsnp_rod_bind_type"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &lt;dbsnp&gt;"> + <option value="set_dbsnp" selected="True">Set dbSNP</option> + <option value="exclude_dbsnp">Don't set dbSNP</option> + </param> + <when value="exclude_dbsnp"> + <!-- Do nothing here --> + </when> + <when value="set_dbsnp"> + <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" /> + <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/> + <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" help="-knownName,--known_names &lt;known_names&gt;" /> + </when> + </conditional> + + <expand macro="gatk_param_type_conditional" /> + + + <expand macro="analysis_type_conditional"> + <repeat name="stratifications" title="Stratification"> + <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &lt;select_exps&gt;"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &lt;select_names&gt;"/> + </repeat> + + <repeat name="samples" title="Sample" help="-sn,--sample &lt;sample&gt;"> + <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"/> + </repeat> + + <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &lt;stratificationModule&gt;" > + <!-- do these need individual options also? gatk wiki has little info --> + <option value="AlleleFrequency" /> + <option value="AlleleCount" /> + <option value="CompRod" /> + <option value="Contig" /> + <option value="CpG" /> + <option value="Degeneracy" /> + <option value="EvalRod" /> + <option value="Filter" /> + <option value="FunctionalClass" /> + <option value="JexlExpression" /> + <option value="Sample" /> + <option value="IntervalStratification" /> + </param> + <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" /> + + <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType"> + <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/> + </repeat> + + <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &lt;evalModule&gt;" > + <!-- do these need individual options also? gatk wiki has little info --> + <option value="ACTransitionTable" /> + <option value="AlleleFrequencyComparison" /> + <option value="AminoAcidTransition" /> + <option value="CompOverlap" /> + <option value="CountVariants" /> + <option value="GenotypeConcordance" /> + <option value="GenotypePhasingEvaluator" /> + <option value="IndelMetricsByAC" /> + <option value="IndelStatistics" /> + <option value="MendelianViolationEvaluator" /> + <option value="PrintMissingComp" /> + <option value="PrivatePermutations" /> + <option value="SimpleMetricsByAC" /> + <option value="ThetaVariantEvaluator" /> + <option value="TiTvVariantEvaluator" /> + <option value="VariantQualityScore" /> + </param> + <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" /> + + <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 &lt;numSamples&gt;"/> + <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &lt;minPhaseQuality&gt;"/> + <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"/> + <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 &lt;mendelianViolationQualThreshold&gt;"/> + <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &lt;ancestralAlignments&gt;" /> + <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 &lt;knownCNVs&gt;" /> + <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 &lt;stratIntervals&gt;" /> + + </expand> + + + </inputs> + <outputs> + <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" /> + <data format="txt" name="output_log" label="${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="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> + <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> + <param name="dbsnp_known_names" value="True"/> + <param name="comp_rod_bind" value="0" /> + <param name="gatk_param_type_selector" value="basic" /> + <param name="analysis_param_type_selector" value="basic" /> + <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" /> + <output name="output_log" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains" compare="contains" /> + </test> + </tests> + <help> +**What it does** + +General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) + +For more information on using the VariantEval module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval>`_. + +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: VariantEval accepts variant files as input. + + +**Outputs** + +The output is a table of variant evaluation. + + +Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. + + +------- + +**Settings**:: + + out An output file presented to the walker. Will overwrite contents if file exists. + list List the available eval modules and exit + select_exps One or more stratifications to use when evaluating the data + select_names Names to use for the list of stratifications (must be a 1-to-1 mapping) + sample Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context + known_names Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets + stratificationModule One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) + doNotUseAllStandardStratifications Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) + onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in + evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified) + doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option) + numSamples Number of samples (used if no samples are available in the VCF file + minPhaseQuality Minimum phasing quality + 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 + mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation + ancestralAlignments Fasta file with ancestral alleles + +@CITATION_SECTION@ + </help> +</tool>