Mercurial > repos > iuc > gatk2
diff haplotype_caller.xml @ 0:340633249b3d draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 02 Dec 2013 06:18:36 -0500 |
| parents | |
| children | 8bcc13094767 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/haplotype_caller.xml Mon Dec 02 06:18:36 2013 -0500 @@ -0,0 +1,348 @@ +<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.7"> + <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description> + <expand macro="requirements" /> + <macros> + <import>gatk2_macros.xml</import> + </macros> + <command interpreter="python"> + gatk2_wrapper.py + --stdout "${output_log}" + -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" + #if str( $reference_source.input_bam.metadata.bam_index ) != "None": + -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index + #end if + -p ' + @JAR_PATH@ + -T "HaplotypeCaller" + -o "${output_vcf}" + + \$GATK2_SITE_OPTIONS + + @THREADS@ + + #if $reference_source.reference_source_selector != "history": + -R "${reference_source.ref_file.fields.path}" + #end if + #if str($input_recal) != 'None': + --BQSR "${input_recal}" + #end if + ' + #include source=$standard_gatk_options# + + ##start analysis specific options + #if $analysis_param_type.analysis_param_type_selector == "advanced": + -p ' + #if $analysis_param_type.p_nonref_model.__str__ != "None" and len($analysis_param_type.p_nonref_model.__str__) > 0: + --p_nonref_model $analysis_param_type.p_nonref_model + #end if + #if $analysis_param_type.heterozygosity.__str__.strip() != '': + --heterozygosity $analysis_param_type.heterozygosity + #end if + --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}" + #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES': + --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}" + #end if + #if $analysis_param_type.output_mode.__str__ != "None" and len($analysis_param_type.output_mode.__str__) > 0: + --output_mode $analysis_param_type.output_mode + #end if + + ## files + #if str($analysis_param_type.activeRegionIn) != 'None': + --activeRegionIn "$analysis_param_type.activeRegionIn" + #end if + #if str($analysis_param_type.comp) != 'None': + --comp "$analysis_param_type.comp" + #end if + #if str($analysis_param_type.dbsnp) != 'None': + --dbsnp "$analysis_param_type.dbsnp" + #end if + ## + #if str( $analysis_param_type.annotation ) != "None": + #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','): + --annotation "${annotation}" + #end for + #end if + #for $additional_annotation in $analysis_param_type.additional_annotations: + --annotation "${additional_annotation.additional_annotation_name}" + #end for + #if str( $analysis_param_type.group ) != "None": + #for $group in str( $analysis_param_type.group ).split( ','): + --group "${group}" + #end for + #end if + #if str( $analysis_param_type.exclude_annotations ) != "None": + #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','): + --excludeAnnotation "${annotation}" + #end for + #end if + + ## value setings + #if $analysis_param_type.contamination_fraction_to_filter.__str__.strip() != '': + --contamination_fraction_to_filter $analysis_param_type.contamination_fraction_to_filter + #end if + #if $analysis_param_type.downsampleRegion.__str__.strip() != '': + --downsampleRegion $analysis_param_type.downsampleRegion + #end if + #if $analysis_param_type.minPruning.__str__.strip() != '': + --minPruning $analysis_param_type.minPruning + #end if + #if $analysis_param_type.standard_min_confidence_threshold_for_calling.__str__.strip() != '': + --standard_min_confidence_threshold_for_calling $analysis_param_type.standard_min_confidence_threshold_for_calling + #end if + #if $analysis_param_type.standard_min_confidence_threshold_for_emitting.__str__.strip() != '': + --standard_min_confidence_threshold_for_emitting $analysis_param_type.standard_min_confidence_threshold_for_emitting + #end if + #if $analysis_param_type.gcpHMM.__str__.strip() != '': + --gcpHMM $analysis_param_type.gcpHMM + #end if + #if $analysis_param_type.max_alternate_alleles.__str__.strip() != '': + --max_alternate_alleles $analysis_param_type.max_alternate_alleles + #end if + ## mode selections + #if $analysis_param_type.genotyping_mode.__str__ != "None" and len($analysis_param_type.genotyping_mode.__str__) > 0: + --genotyping_mode $analysis_param_type.genotyping_mode + #end if + #if $analysis_param_type.pair_hmm_implementation.__str__ != "None" and len($analysis_param_type.pair_hmm_implementation.__str__) > 0: + --pair_hmm_implementation $analysis_param_type.pair_hmm_implementation + #end if + ## optional outputs + #if $analysis_param_type.activeRegionOut: + --activeRegionOut $active_region_out + #end if + #if $analysis_param_type.graphOutput: + --graphOutput $graph_out + #end if + ## flags + $analysis_param_type.useAllelesTrigger + $analysis_param_type.fullHaplotype + $analysis_param_type.genotypeFullActiveRegion + $analysis_param_type.debug + ' + #end if + </command> + <inputs> + <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &lt;recal_file&gt;" > + <help>The input covariates table file which enables on-the-fly base quality score recalibration. + Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. + Please be aware that one should only run recalibration with the covariates file created on the same input bam(s). + </help> + </param> + <conditional name="reference_source"> + <expand macro="reference_source_selector_param" /> + <when value="cached"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> + </param> + <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_bam" 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"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"> + <options> + <filter type="data_meta" key="dbkey" ref="input_bam" /> + </options> + </param> + </when> + </conditional> + + <expand macro="gatk_param_type_conditional" /> + + <conditional name="analysis_param_type"> + <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> + <!-- Do nothing here --> + </when> + <when value="advanced"> + + <param name="activeRegionIn" type="data" format="bed,gatk_interval,picard_interval_list,vcf" optional="true" label="activeRegionIn" help="--activeRegionIn / -AR Use this interval list file as the active regions to process"/> + <param name="activeRegionOut" type="boolean" checked="False" truevalue="" falsevalue="" label="activeRegionOut" help="--activeRegionOut / -ARO Output the active region to an interval list file"/> + + <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> + <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> + <options from_data_table="gatk2_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + </options> + </param> + <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> + <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> + </repeat> +<!-- + <conditional name="snpEff_rod_bind_type"> + <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> + <option value="set_snpEff">Set snpEff</option> + <option value="exclude_snpEff" selected="True">Don't set snpEff</option> + </param> + <when value="exclude_snpEff"> + </when> + <when value="set_snpEff"> + <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" /> + <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/> + </when> + </conditional> +--> + <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &lt;group&gt;"> + <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> + <option value="Standard">Standard</option> + <option value="Experimental">Experimental</option> + <option value="WorkInProgress">WorkInProgress</option> + <option value="RankSumTest">RankSumTest</option> + <!-- <option value="none">none</option> --> + </param> + <!-- <param name="family_string" type="text" value="" label="Family String"/> --> + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > + <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> + <options from_data_table="gatk2_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + </options> + </param> + + <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp comparison VCF file"/> + <param name="contamination_fraction_to_filter" type="float" value="0.05" optional="true" label="contamination_fraction_to_filter" help="--contamination_fraction_to_filter / -contamination Fraction of contamination in sequencing data (for all samples) to aggressively remove"> + <validator type="in_range" message="value between 0.00 and 1.00" min="0" max="1"/> + </param> + <param name="dbsnp" type="data" format="vcf" optional="true" label="dbsnp" help="--dbsnp / -D dbSNP file"/> + <param name="debug" type="boolean" checked="False" truevalue="-debug" falsevalue="" label="debug" help="--debug / -debug If specified, print out very verbose debug information about each triggering active region"/> + <param name="downsampleRegion" type="integer" value="1000" optional="true" label="downsampleRegion" help="--downsampleRegion / -dr coverage, per-sample, to downsample each active region to"/> + + <conditional name="genotyping_mode_type"> + <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &lt;genotyping_mode&gt;"> + <option value="DISCOVERY" selected="True">DISCOVERY</option> + <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> + </param> + <when value="DISCOVERY"> + <!-- Do nothing here --> + </when> + <when value="GENOTYPE_GIVEN_ALLELES"> + <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &lt;alleles&gt;" /> + </when> + </conditional> + + + <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph File to which debug assembly graph information should be written"/> + <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets Heterozygosity value used to compute prior likelihoods for any locus"/> + <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning The minimum allowed pruning factor in assembly graph. Paths with >= X supporting kmers are pruned from the graph"> + <validator type="in_range" message="value between 0 and 127" min="0" max="127"/> + </param> + <param name="output_mode" type="select" optional="true" label="output_mode" help="--output_mode / -out_mode Specifies which type of calls we should output"> + <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option> + <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option> + <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option> + </param> + <param name="pair_hmm_implementation" type="select" optional="true" label="pair_hmm_implementation" help="--pair_hmm_implementation / -pairHMM The PairHMM implementation to use for genotype likelihood calculations"> + <option value="EXACT">EXACT</option> + <option value="ORIGINAL">ORIGINAL</option> + <option value="CACHING">CACHING</option> + <option value="LOGLESS_CACHING" selected="True">LOGLESS_CACHING</option> + </param> + <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" optional="true" label="standard_min_confidence_threshold_for_calling" help="--standard_min_confidence_threshold_for_calling / -stand_call_conf The minimum phred-scaled confidence threshold at which variants should be called"/> + <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" optional="true" label="standard_min_confidence_threshold_for_emitting" help="--standard_min_confidence_threshold_for_emitting / -stand_emit_conf The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)"/> + <param name="useAllelesTrigger" type="boolean" checked="False" truevalue="-allelesTrigger" falsevalue="" label="useAllelesTrigger" help="--useAllelesTrigger / -allelesTrigger If specified, use additional trigger on variants found in an external alleles file"/> + <param name="fullHaplotype" type="boolean" checked="False" truevalue="-fullHaplotype" falsevalue="" label="fullHaplotype" help="--fullHaplotype / -fullHaplotype If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference"/> + <param name="gcpHMM" type="integer" value="10" optional="true" label="gcpHMM" help="--gcpHMM / -gcpHMM Flat gap continuation penalty for use in the Pair HMM"/> + <param name="genotypeFullActiveRegion" type="boolean" checked="False" truevalue="-genotypeFullActiveRegion" falsevalue="" label="genotypeFullActiveRegion" help="--genotypeFullActiveRegion / -genotypeFullActiveRegion If specified, alternate alleles are considered to be the full active region for the purposes of genotyping"/> + <param name="max_alternate_alleles" type="integer" value="6" optional="true" label="max_alternate_alleles" help="--max_alternate_alleles / -maxAltAlleles Maximum number of alternate alleles to genotype"/> + <param name="p_nonref_model" type="select" optional="true" label="p_nonref_model" help="--p_nonref_model / -pnrm Non-reference probability calculation model to employ"> + <option value="EXACT_INDEPENDENT" selected="True">EXACT_INDEPENDENT experimental implementation - for testing only</option> + <option value="EXACT_REFERENCE">EXACT_REFERENCE reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles</option> + <option value="EXACT_ORIGINAL">EXACT_ORIGINAL original biallelic exact model, for testing only</option> + <option value="EXACT_GENERAL_PLOIDY">implementation that supports any sample ploidy</option> + </param> + + </when> + </conditional> + </inputs> + <outputs> + <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> + <data format="vcf" name="graph_out" label="${tool.name} on ${on_string} graph" > + <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['graphOutput'] == True</filter> + </data> + <data format="vcf" name="active_region_out" label="${tool.name} on ${on_string} activeRegion" > + <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['activeRegionOut'] == True</filter> + </data> + <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> + </outputs> + <tests> + <test> + <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="phiX.fasta" ftype="fasta" /> + <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /> + <param name="gatk_param_type_selector" value="basic" /> + <param name="analysis_param_type_selector" value="basic" /> + <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" /> + <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" /> + </test> + </tests> + <help> +**What it does** + +**HaplotypeCaller** +calls SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. +Haplotypes are evaluated using an affine gap penalty Pair HMM. + +For more information on using read based compression in the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.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: PrintReads accepts aligned BAM files. + + +**Outputs** + +The output is a VCF file with raw, unrecalibrated SNP and indel calls. + + +Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. + +------- + +**Settings**:: + + activeRegionIn Use this interval list file as the active regions to process + activeRegionOut Output the active region to this interval list file + alleles The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES + annotation One or more specific annotations to apply to variant calls + comp comparison VCF file + contamination Fraction of contamination in sequencing data (for all samples) to aggressively remove + dbsnp dbSNP file + debug If specified, print out very verbose debug information about each triggering active region + downsampleRegion coverage, per-sample, to downsample each active region to + excludeAnnotation One or more specific annotations to exclude + genotyping_mode Specifies how to determine the alternate alleles to use for genotyping + graphOutput File to which debug assembly graph information should be written + group One or more classes/groups of annotations to apply to variant calls + heterozygosity Heterozygosity value used to compute prior likelihoods for any locus + minPruning The minimum allowed pruning factor in assembly graph. Paths with less than or equal supporting kmers are pruned from the graph + output_mode Specifies which type of calls we should output + pair_hmm_implementation The PairHMM implementation to use for genotype likelihood calculations + stand_call_conf The minimum phred-scaled confidence threshold at which variants should be called + stand_emit_conf The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold) + useAllelesTrigger If specified, use additional trigger on variants found in an external alleles file + fullHaplotype If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference + gcpHMM Flat gap continuation penalty for use in the Pair HMM + genotypeFullActiveRegion If specified, alternate alleles are considered to be the full active region for the purposes of genotyping + max_alternate_alleles Maximum number of alternate alleles to genotype + p_nonref_model Non-reference probability calculation model to employ + +------ + +@CITATION_SECTION@ + </help> +</tool>