Mercurial > repos > jjohnson > gatk2
changeset 32:fd9d089a9ff4 draft
unified_genotyper - add sample_poidy param
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Feb 2013 12:45:44 -0600 |
| parents | a5c55503d196 |
| children | 76f8ca47b810 |
| files | unified_genotyper.xml |
| diffstat | 1 files changed, 11 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/unified_genotyper.xml Thu Feb 28 12:44:55 2013 -0600 +++ b/unified_genotyper.xml Thu Feb 28 12:45:44 2013 -0600 @@ -5,6 +5,7 @@ <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <command interpreter="python">gatk2_wrapper.py + #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter'] --max_jvm_heap_fraction "1" --stdout "${output_log}" #for $i, $input_bam in enumerate( $reference_source.input_bams ): @@ -52,7 +53,10 @@ #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: - -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" + -p ' + #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: + --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" + #end_if ###raise Exception( str( dir( $read_filter ) ) ) #for $name, $param in $read_filter.read_filter_type.iteritems(): #if $name not in [ "__current_case__", "read_filter_type_selector" ]: @@ -143,6 +147,9 @@ #end for #end if ${analysis_param_type.multiallelic} + #if str( $analysis_param_type.sample_ploidy ) != '': + --sample_ploidy "$analysis_param_type.sample_ploidy" + #end if ' ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': ## -p '--annotation "SnpEff"' @@ -510,6 +517,9 @@ </options> </param> <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" /> + <param name="sample_ploidy" type="integer" value="" optional="true" label="Ploidy (number of chromosomes) per sample." help="--sample_ploidy / -ploidy (default value 2 ). For pooled data, set to (Number of samples in each pool * Sample Ploidy)."> + <validator type="in_range" message="Ploidy must be at least 1" min="1" /> + </param> </when> </conditional> </inputs>