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comparison kggseq_variant_selection.xml @ 7:dc45e612bc47 draft

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Updates to KGGSeq 1.0_20180410
author crs4
date Mon, 11 Jun 2018 12:40:53 -0400
parents a13b8ff61c6c
children
comparison
equal deleted inserted replaced
6:4e47d0245887 7:dc45e612bc47
1 <tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.4"> 1 <tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.5">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0_0_20160412">kggseq</requirement> 4 <requirement type="package" version="1.0_20180410">kggseq</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 java -jar \$KGGSEQ_JAR_PATH/kggseq.jar 7 java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
8 ## Environmental settings 8 ## Environmental settings
9 --buildver hg19 9 --buildver hg19
303 <option value="dbsnp138">dbSNP 138</option> 303 <option value="dbsnp138">dbSNP 138</option>
304 <option value="dbsnp138nf">dbSNP 138nf: dbSNP version 138 without the flagged SNPs by UCSC. Flagged SNPs include SNPs clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%</option> 304 <option value="dbsnp138nf">dbSNP 138nf: dbSNP version 138 without the flagged SNPs by UCSC. Flagged SNPs include SNPs clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%</option>
305 <option value="dbsnp137">dbSNP 137</option> 305 <option value="dbsnp137">dbSNP 137</option>
306 <option value="dbsnp135">dbSNP 135</option> 306 <option value="dbsnp135">dbSNP 135</option>
307 <option value="exac">Exome Aggregation Consortium (ExAC): Variants from 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies</option> 307 <option value="exac">Exome Aggregation Consortium (ExAC): Variants from 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies</option>
308 <option value="gadexome">Genome Aggregation Database - Exome (gnomAD): Variants from 123,136 exomes sequenced as part of various disease-specific and population genetic studies</option>
309 <option value="gadgenome">Genome Aggregation Database - Genome (gnomAD): Variants from 15,496 whole-genomes sequenced as part of various disease-specific and population genetic studies</option>
308 </param> 310 </param>
309 <param name="rare_allele_freq" type="float" value="0.01" label="Minor allele frequency (MAF) for selecting rare variants (--rare-allele-freq)" help="Set to &gt;1 to only annotate MAF, without filtering" /> 311 <param name="rare_allele_freq" type="float" value="0.01" label="Minor allele frequency (MAF) for selecting rare variants (--rare-allele-freq)" help="Set to &gt;1 to only annotate MAF, without filtering" />
310 </when> 312 </when>
311 <when value="no" /> 313 <when value="no" />
312 </conditional> 314 </conditional>
343 <option value="yes">Yes</option> 345 <option value="yes">Yes</option>
344 <option value="no" selected="true">No</option> 346 <option value="no" selected="true">No</option>
345 </param> 347 </param>
346 <when value="yes"> 348 <when value="yes">
347 <param name="filter_nondisease_variant" type="boolean" truevalue="--filter-nondisease-variant" falsevalue="" checked="false" label="Filter out variants predicted to be non-disease causal (--filter-nondisease-variant)" /> 349 <param name="filter_nondisease_variant" type="boolean" truevalue="--filter-nondisease-variant" falsevalue="" checked="false" label="Filter out variants predicted to be non-disease causal (--filter-nondisease-variant)" />
348 <param name="mendel_causing" type="boolean" truevalue="--mendel-causing-predict all" falsevalue="" checked="true" label="Predict Mendelian disease-causing variants by logistic regression model (--mendel-causing-predict)" /> 350 <param name="mendel_causing" type="boolean" truevalue="--mendel-causing-predict best" falsevalue="" checked="true" label="Predict Mendelian disease-causing variants by logistic regression model (--mendel-causing-predict)" />
349 </when> 351 </when>
350 <when value="no" /> 352 <when value="no" />
351 </conditional> 353 </conditional>
352 354
353 <!-- Annotations --> 355 <!-- Annotations -->