| Previous changeset 6:4e47d0245887 (2016-08-05) Next changeset 8:eebc0adefae0 (2018-06-11) |
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Commit message:
Updates to KGGSeq 1.0_20180410 |
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modified:
kggseq_variant_selection.xml |
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| diff -r 4e47d0245887 -r dc45e612bc47 kggseq_variant_selection.xml --- a/kggseq_variant_selection.xml Fri Aug 05 06:05:03 2016 -0400 +++ b/kggseq_variant_selection.xml Mon Jun 11 12:40:53 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.4"> +<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.5"> <description></description> <requirements> - <requirement type="package" version="1.0_0_20160412">kggseq</requirement> + <requirement type="package" version="1.0_20180410">kggseq</requirement> </requirements> <command> java -jar \$KGGSEQ_JAR_PATH/kggseq.jar @@ -305,6 +305,8 @@ <option value="dbsnp137">dbSNP 137</option> <option value="dbsnp135">dbSNP 135</option> <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> + <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> + <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> </param> <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 >1 to only annotate MAF, without filtering" /> </when> @@ -345,7 +347,7 @@ </param> <when value="yes"> <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)" /> - <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)" /> + <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)" /> </when> <when value="no" /> </conditional> |