--- a/kggseq_variant_selection.xml	Tue Apr 28 12:35:35 2015 -0400
+++ b/kggseq_variant_selection.xml	Mon May 25 18:01:25 2015 -0400
@@ -1,7 +1,7 @@
-<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.2">
+<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.3">
   <description></description>
   <requirements>
-    <requirement type="package" version="0.7_20150118">kggseq</requirement>
+    <requirement type="package" version="0.8_20150423 ">kggseq</requirement>
   </requirements>
   <command>
 java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
@@ -20,8 +20,8 @@
 $composite_subject_id
 
 ## Variant and genotype filters
-$pass_variant_only
 #if str($variant_genotype_filters.variant_genotype_filters_select) == "yes"
+  $variant_genotype_filters.pass_variant_only
   --seq-qual $variant_genotype_filters.seq_qual
   --seq-mq $variant_genotype_filters.seq_mq
   --seq-sb $variant_genotype_filters.seq_sb
@@ -150,7 +150,6 @@
       <option value="ensembl">ensembl: The Ensembl gene datasase compiled by UCSC from hg19 ensGene</option>
       <validator type="no_options" message="Select at least one database" />
     </param>
-    <param name="pass_variant_only" type="boolean" truevalue="--vcf-filter-in PASS" falsevalue="" checked="true" label="Don't include filtered loci (--vcf-filter-in PASS)" help="Keep only variants with FILTER equal to PASS" />
 
     <!-- Variant and genotype quality control -->
     <conditional name="variant_genotype_filters">
@@ -159,6 +158,7 @@
         <option value="no" selected="true">No</option>
       </param>
       <when value="yes">
+        <param name="pass_variant_only" type="boolean" truevalue="--vcf-filter-in PASS" falsevalue="" checked="true" label="Don't include filtered loci (--vcf-filter-in PASS)" help="Keep only variants with FILTER equal to PASS" />
         <param name="seq_qual" type="integer" value="50" label="Minimum overall Phred-scaled sequencing quality score for the variant (--seq-qual)" />
         <param name="seq_mq" type="integer" value="20" label="Minimum overall Phred-scaled mapping quality score for the variant (--seq-mq)" />
         <param name="seq_sb" type="float" value="-10" label="Maximal overall strand bias score for the variant (--seq-sb)" />
@@ -247,21 +247,22 @@
         <param name="gene_features" type="select" display="checkboxes" multiple="true" label="Select gene features (--gene-feature-in)" help="Variants falling outside the selected regions will be excluded">
           <option value="0" selected="true">Frame-shift</option>
           <option value="1" selected="true">Loss of amino acids</option>
-          <option value="2" selected="true">Loss of stop codon (TAG, TAA, TGA)</option>
-          <option value="3" selected="true">Gain of stop codon (TAG, TAA, TGA)</option>
-          <option value="4" selected="true">Missense</option>
+          <option value="2" selected="true">Loss of start codon</option>
+          <option value="3" selected="true">Loss of stop codon (TAG, TAA, TGA)</option>
+          <option value="4" selected="true">Gain of stop codon (TAG, TAA, TGA)</option>
           <option value="5" selected="true">Splicing</option>
-          <option value="6">Synonymous</option>
-          <option value="7">Exonic</option>
-          <option value="8">5-UTR</option>
-          <option value="9">3-UTR</option>
-          <option value="10">Intronic</option>
-          <option value="11">Upstream of transcription start site</option>
-          <option value="12">Downstream of transcription end site</option>
-          <option value="13">ncRNA</option>
-          <option value="14">Intergenic</option>
-          <option value="15">Monomorphic</option>
-          <option value="16">Unknown</option>
+          <option value="6" selected="true">Missense</option>
+          <option value="7">Synonymous</option>
+          <option value="8">Exonic</option>
+          <option value="9">5-UTR</option>
+          <option value="10">3-UTR</option>
+          <option value="11">Intronic</option>
+          <option value="12">Upstream of transcription start site</option>
+          <option value="13">Downstream of transcription end site</option>
+          <option value="14">ncRNA</option>
+          <option value="15">Intergenic</option>
+          <option value="16">Monomorphic</option>
+          <option value="17">Unknown</option>
         </param>
         <param name="splicing" type="integer" value="2" label="Window size in base-pair around the splicing junction to flag the variant as splicing (--splicing)" />
         <param name="neargene" type="integer" value="1000" label="Size in base-pair of region upstream and downstream (--neargene)" />

--- a/tool_dependencies.xml	Tue Apr 28 12:35:35 2015 -0400
+++ b/tool_dependencies.xml	Mon May 25 18:01:25 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="kggseq" version="0.7_20150118">
+  <package name="kggseq" version="0.8_20150423">
     <install version="1.0">
       <actions>
-        <action type="download_by_url" target_filename="kggseq_archive-0.7_20150118.tar.gz">https://github.com/crs4/kggseq_archive/archive/v0.7_20150118.tar.gz</action>
+        <action type="download_by_url" target_filename="kggseq_archive-v0.8_20150423.tar.gz">https://github.com/crs4/kggseq_archive/archive/v0.8_20150423.tar.gz</action>
         <action type="shell_command">touch test.vcf</action>
         <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --vcf-file test.vcf</action>
         <action type="shell_command">java -Xmx4g -jar kggseq.jar --no-lib-check --no-qc --resource resources --buildver hg19 --o-flanking-seq 10 --vcf-file examples/rare.disease.hg19.vcf</action>