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comparison haplotype_caller.xml @ 17:f2b21dc45241 draft

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Many fixes to haplotype_caller
author Jim Johnson <jj@umn.edu>
date Thu, 15 Nov 2012 10:18:55 -0600
parents d73c92a7b0ea
children 7533db8dfb5b
comparison
equal deleted inserted replaced
16:d56503a12975 17:f2b21dc45241
87 ##end standard gatk options 87 ##end standard gatk options
88 88
89 ##start analysis specific options 89 ##start analysis specific options
90 #if $analysis_param_type.analysis_param_type_selector == "advanced": 90 #if $analysis_param_type.analysis_param_type_selector == "advanced":
91 -p ' 91 -p '
92 #if $analysis_param_type.p_nonref_model.__str__ != "None" and len($analysis_param_type.p_nonref_model.__str__) > 0:
93 --p_nonref_model $analysis_param_type.p_nonref_model
94 #end if
95 #if $analysis_param_type.heterozygosity.__str__.strip() != '':
96 --heterozygosity $analysis_param_type.heterozygosity
97 #end if
98 --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}"
99 #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES':
100 --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}"
101 #end if
102 #if $analysis_param_type.output_mode.__str__ != "None" and len($analysis_param_type.output_mode.__str__) > 0:
103 --output_mode $analysis_param_type.output_mode
104 #end if
105
92 ## files 106 ## files
93 #if str($analysis_param_type.activeRegionIn) != 'None': 107 #if str($analysis_param_type.activeRegionIn) != 'None':
94 --activeRegionIn "$analysis_param_type.activeRegionIn" 108 --activeRegionIn "$analysis_param_type.activeRegionIn"
95 #end if 109 #end if
96 #if str($analysis_param_type.alleles) != 'None':
97 --alleles "$analysis_param_type.alleles"
98 #end if
99 #if str($analysis_param_type.comp) != 'None': 110 #if str($analysis_param_type.comp) != 'None':
100 --comp "$analysis_param_type.comp" 111 --comp "$analysis_param_type.comp"
101 #end if 112 #end if
102 #if str($analysis_param_type.dbsnp) != 'None': 113 #if str($analysis_param_type.dbsnp) != 'None':
103 --dbsnp "$analysis_param_type.dbsnp" 114 --dbsnp "$analysis_param_type.dbsnp"
104 #end if 115 #end if
105 ## text 116 ##
106 #if len($analysis_param_type.annotation.__str__) > 0: 117 #if str( $analysis_param_type.annotation ) != "None":
107 --annotation $analysis_param_type.annotation 118 #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
108 #end if 119 --annotation "${annotation}"
109 #if len($analysis_param_type.excludeAnnotation.__str__) > 0: 120 #end for
110 --excludeAnnotation $analysis_param_type.excludeAnnotation 121 #end if
111 #end if 122 #for $additional_annotation in $analysis_param_type.additional_annotations:
112 #if len($analysis_param_type.group.__str__) > 0: 123 --annotation "${additional_annotation.additional_annotation_name}"
113 --group $analysis_param_type.group 124 #end for
114 #end if 125 #if str( $analysis_param_type.group ) != "None":
126 #for $group in str( $analysis_param_type.group ).split( ','):
127 --group "${group}"
128 #end for
129 #end if
130 #if str( $analysis_param_type.exclude_annotations ) != "None":
131 #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','):
132 --excludeAnnotation "${annotation}"
133 #end for
134 #end if
135
115 ## value setings 136 ## value setings
116 #if $analysis_param_type.contamination_fraction_to_filter.__str__.strip() != '': 137 #if $analysis_param_type.contamination_fraction_to_filter.__str__.strip() != '':
117 --contamination_fraction_to_filter $analysis_param_type.contamination_fraction_to_filter 138 --contamination_fraction_to_filter $analysis_param_type.contamination_fraction_to_filter
118 #end if 139 #end if
119 #if $analysis_param_type.downsampleRegion.__str__.strip() != '': 140 #if $analysis_param_type.downsampleRegion.__str__.strip() != '':
120 --downsampleRegion $analysis_param_type.downsampleRegion 141 --downsampleRegion $analysis_param_type.downsampleRegion
121 #end if 142 #end if
122 #if $analysis_param_type.heterozygosity.__str__.strip() != '':
123 --heterozygosity $analysis_param_type.heterozygosity
124 #end if
125 #if $analysis_param_type.minPruning.__str__.strip() != '': 143 #if $analysis_param_type.minPruning.__str__.strip() != '':
126 --minPruning $analysis_param_type.minPruning 144 --minPruning $analysis_param_type.minPruning
127 #end if 145 #end if
128 #if $analysis_param_type.standard_min_confidence_threshold_for_calling.__str__.strip() != '': 146 #if $analysis_param_type.standard_min_confidence_threshold_for_calling.__str__.strip() != '':
129 --standard_min_confidence_threshold_for_calling $analysis_param_type.standard_min_confidence_threshold_for_calling 147 --standard_min_confidence_threshold_for_calling $analysis_param_type.standard_min_confidence_threshold_for_calling
139 #end if 157 #end if
140 ## mode selections 158 ## mode selections
141 #if $analysis_param_type.genotyping_mode.__str__ != "None" and len($analysis_param_type.genotyping_mode.__str__) > 0: 159 #if $analysis_param_type.genotyping_mode.__str__ != "None" and len($analysis_param_type.genotyping_mode.__str__) > 0:
142 --genotyping_mode $analysis_param_type.genotyping_mode 160 --genotyping_mode $analysis_param_type.genotyping_mode
143 #end if 161 #end if
144 #if $analysis_param_type.output_mode.__str__ != "None" and len($analysis_param_type.output_mode.__str__) > 0:
145 --output_mode $analysis_param_type.output_mode
146 #end if
147 #if $analysis_param_type.pair_hmm_implementation.__str__ != "None" and len($analysis_param_type.pair_hmm_implementation.__str__) > 0: 162 #if $analysis_param_type.pair_hmm_implementation.__str__ != "None" and len($analysis_param_type.pair_hmm_implementation.__str__) > 0:
148 --pair_hmm_implementation $analysis_param_type.pair_hmm_implementation 163 --pair_hmm_implementation $analysis_param_type.pair_hmm_implementation
149 #end if
150 #if $analysis_param_type.p_nonref_model.__str__ != "None" and len($analysis_param_type.p_nonref_model.__str__) > 0:
151 --p_nonref_model $analysis_param_type.p_nonref_model
152 #end if 164 #end if
153 ## optional outputs 165 ## optional outputs
154 #if $analysis_param_type.activeRegionOut: 166 #if $analysis_param_type.activeRegionOut:
155 --activeRegionOut $active_region_out 167 --activeRegionOut $active_region_out
156 #end if 168 #end if
164 $analysis_param_type.debug 176 $analysis_param_type.debug
165 ' 177 '
166 #end if 178 #end if
167 </command> 179 </command>
168 <inputs> 180 <inputs>
169 <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" > 181 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" >
170 <help>The input covariates table file which enables on-the-fly base quality score recalibration. 182 <help>The input covariates table file which enables on-the-fly base quality score recalibration.
171 Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. 183 Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool.
172 Please be aware that one should only run recalibration with the covariates file created on the same input bam(s). 184 Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
173 </help> 185 </help>
174 </param> 186 </param>
419 </when> 431 </when>
420 <when value="advanced"> 432 <when value="advanced">
421 433
422 <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"/> 434 <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"/>
423 <param name="activeRegionOut" type="boolean" checked="False" truevalue="" falsevalue="" label="activeRegionOut" help="--activeRegionOut / -ARO Output the active region to an interval list file"/> 435 <param name="activeRegionOut" type="boolean" checked="False" truevalue="" falsevalue="" label="activeRegionOut" help="--activeRegionOut / -ARO Output the active region to an interval list file"/>
424 <param name="alleles" type="data" format="vcf" optional="true" label="alleles" help="--alleles / -alleles The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES"/> 436
425 <param name="annotation" type="text" value="" optional="true" label="annotation" help="--annotation / -A One or more specific annotations to apply to variant calls default: ClippingRankSumTest"/> 437 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;annotation&amp;gt;">
438 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
439 <options from_data_table="gatk2_annotations">
440 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
441 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
442 </options>
443 </param>
444 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
445 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
446 </repeat>
447 <!--
448 <conditional name="snpEff_rod_bind_type">
449 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
450 <option value="set_snpEff">Set snpEff</option>
451 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
452 </param>
453 <when value="exclude_snpEff">
454 </when>
455 <when value="set_snpEff">
456 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
457 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
458 </when>
459 </conditional>
460 -->
461 <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &amp;lt;group&amp;gt;">
462 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
463 <option value="Standard">Standard</option>
464 <option value="Experimental">Experimental</option>
465 <option value="WorkInProgress">WorkInProgress</option>
466 <option value="RankSumTest">RankSumTest</option>
467 <!-- <option value="none">none</option> -->
468 </param>
469 <!-- <param name="family_string" type="text" value="" label="Family String"/> -->
470 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
471 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
472 <options from_data_table="gatk2_annotations">
473 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
474 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
475 </options>
476 </param>
477
426 <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp comparison VCF file"/> 478 <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp comparison VCF file"/>
427 <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"> 479 <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">
428 <validator type="in_range" message="value between 0.00 and 1.00" min="0" max="1"/> 480 <validator type="in_range" message="value between 0.00 and 1.00" min="0" max="1"/>
429 </param> 481 </param>
430 <param name="dbsnp" type="data" format="vcf" optional="true" label="dbsnp" help="--dbsnp / -D dbSNP file"/> 482 <param name="dbsnp" type="data" format="vcf" optional="true" label="dbsnp" help="--dbsnp / -D dbSNP file"/>
431 <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"/> 483 <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"/>
432 <param name="downsampleRegion" type="integer" value="1000" optional="true" label="downsampleRegion" help="--downsampleRegion / -dr coverage, per-sample, to downsample each active region to"/> 484 <param name="downsampleRegion" type="integer" value="1000" optional="true" label="downsampleRegion" help="--downsampleRegion / -dr coverage, per-sample, to downsample each active region to"/>
433 <param name="excludeAnnotation" type="text" optional="true" label="excludeAnnotation" help="--excludeAnnotation / -XA One or more specific annotations to exclude"/> 485
434 <param name="genotyping_mode" type="select" optional="true" label="genotyping_mode" help="--genotyping_mode / -gt_mode Specifies how to determine the alternate alleles to use for genotyping"> 486 <conditional name="genotyping_mode_type">
435 <option value="DISCOVERY" selected="True">DISCOVERY</option> 487 <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &amp;lt;genotyping_mode&amp;gt;">
436 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> 488 <option value="DISCOVERY" selected="True">DISCOVERY</option>
437 </param> 489 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
490 </param>
491 <when value="DISCOVERY">
492 <!-- Do nothing here -->
493 </when>
494 <when value="GENOTYPE_GIVEN_ALLELES">
495 <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" />
496 </when>
497 </conditional>
498
499
438 <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph File to which debug assembly graph information should be written"/> 500 <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph File to which debug assembly graph information should be written"/>
439 <param name="group" type="text" optional="true" label="group" help="--group / -G One or more classes/groups of annotations to apply to variant calls"/>
440 <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"/> 501 <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"/>
441 <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph"> 502 <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph">
442 <validator type="in_range" message="value between 0 and 127" min="0" max="127"/> 503 <validator type="in_range" message="value between 0 and 127" min="0" max="127"/>
443 </param> 504 </param>
444 <param name="output_mode" type="select" optional="true" label="output_mode" help="--output_mode / -out_mode Specifies which type of calls we should output"> 505 <param name="output_mode" type="select" optional="true" label="output_mode" help="--output_mode / -out_mode Specifies which type of calls we should output">