Mercurial > repos > iuc > gatk2
comparison haplotype_caller.xml @ 4:f244b8209eb8 draft
bug fix release
author | iuc |
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date | Mon, 25 Aug 2014 17:43:11 -0400 |
parents | 8bcc13094767 |
children | 35c00763cb5c |
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3:2553f84b8174 | 4:f244b8209eb8 |
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1 <tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.7"> | 1 <tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.0"> |
2 <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description> | 2 <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</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> |
156 | 156 |
157 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> | 157 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> |
158 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | 158 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> |
159 <options from_data_table="gatk2_annotations"> | 159 <options from_data_table="gatk2_annotations"> |
160 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | 160 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> |
161 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> | 161 <filter type="static_value" value="HaplotypeCaller" column="tools_valid_for"/> |
162 </options> | 162 </options> |
163 </param> | 163 </param> |
164 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> | 164 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> |
165 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> | 165 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> |
166 </repeat> | 166 </repeat> |
189 <!-- <param name="family_string" type="text" value="" label="Family String"/> --> | 189 <!-- <param name="family_string" type="text" value="" label="Family String"/> --> |
190 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > | 190 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > |
191 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | 191 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> |
192 <options from_data_table="gatk2_annotations"> | 192 <options from_data_table="gatk2_annotations"> |
193 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | 193 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> |
194 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> | 194 <filter type="static_value" value="HaplotypeCaller" column="tools_valid_for"/> |
195 </options> | 195 </options> |
196 </param> | 196 </param> |
197 | 197 |
198 <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp comparison VCF file"/> | 198 <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp comparison VCF file"/> |
199 <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"> | 199 <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"> |
318 genotypeFullActiveRegion If specified, alternate alleles are considered to be the full active region for the purposes of genotyping | 318 genotypeFullActiveRegion If specified, alternate alleles are considered to be the full active region for the purposes of genotyping |
319 max_alternate_alleles Maximum number of alternate alleles to genotype | 319 max_alternate_alleles Maximum number of alternate alleles to genotype |
320 | 320 |
321 @CITATION_SECTION@ | 321 @CITATION_SECTION@ |
322 </help> | 322 </help> |
323 <expand macro="citations" /> | |
323 </tool> | 324 </tool> |