Mercurial > repos > crs4 > kggseq_variant_selection

changeset 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 4e47d0245887
children eebc0adefae0
files kggseq_variant_selection.xml
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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 &gt;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>