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comparison unified_genotyper.xml @ 4:f244b8209eb8 draft

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bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 2553f84b8174
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
1 <tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.7"> 1 <tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.0">
2 <description>SNP and indel caller</description> 2 <description>SNP and indel caller</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>gatk2_macros.xml</import> 5 <import>gatk2_macros.xml</import>
6 </macros> 6 </macros>
70 #if str( $analysis_param_type.exclude_annotations ) != "None": 70 #if str( $analysis_param_type.exclude_annotations ) != "None":
71 #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','): 71 #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','):
72 --excludeAnnotation "${annotation}" 72 --excludeAnnotation "${annotation}"
73 #end for 73 #end for
74 #end if 74 #end if
75 ${analysis_param_type.multiallelic}
76 #if str( $analysis_param_type.sample_ploidy ) != '': 75 #if str( $analysis_param_type.sample_ploidy ) != '':
77 --sample_ploidy "$analysis_param_type.sample_ploidy" 76 --sample_ploidy "$analysis_param_type.sample_ploidy"
78 #end if 77 #end if
79 ' 78 '
80 ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': 79 ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
197 <options from_data_table="gatk2_annotations"> 196 <options from_data_table="gatk2_annotations">
198 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> 197 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
199 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> 198 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
200 </options> 199 </options>
201 </param> 200 </param>
202 <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" /> 201 <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,--sample_ploidy" />
203 </expand> 202 </expand>
204 </inputs> 203 </inputs>
205 <outputs> 204 <outputs>
206 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> 205 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
207 <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /> 206 <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" />
292 annotation One or more specific annotations to apply to variant calls 291 annotation One or more specific annotations to apply to variant calls
293 group One or more classes/groups of annotations to apply to variant calls 292 group One or more classes/groups of annotations to apply to variant calls
294 293
295 @CITATION_SECTION@ 294 @CITATION_SECTION@
296 </help> 295 </help>
296 <expand macro="citations" />
297 </tool> 297 </tool>