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Changeset 1:e9758eee6697 (2015-04-28)

Previous changeset 0:d388273fb83f (2014-09-12) Next changeset 2:e1a21c2f4997 (2015-04-28)

Commit message:
Update to KggSeq v0.7_20150118

modified:
COPYING
kggseq_variant_selection.xml
tool_dependencies.xml

diff -r d388273fb83f -r e9758eee6697 COPYING
--- a/COPYING Fri Sep 12 21:40:16 2014 -0400
+++ b/COPYING Tue Apr 28 04:42:14 2015 -0400

@@ -1,7 +1,7 @@
-Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/
+Copyright © 2013-2015 CRS4 Srl. http://www.crs4.it/
Created by:
Paolo Uva <paolo.uva@crs4.it>
-Nicola Soranzo <nicola.soranzo@crs4.it>
+Nicola Soranzo <nicola.soranzo@tgac.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the

diff -r d388273fb83f -r e9758eee6697 kggseq_variant_selection.xml
--- a/kggseq_variant_selection.xml Fri Sep 12 21:40:16 2014 -0400
+++ b/kggseq_variant_selection.xml Tue Apr 28 04:42:14 2015 -0400

b'@@ -1,7 +1,7 @@\n-<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.1">\n+<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.2">\n <description></description>\n <requirements>\n- <requirement type="package" version="0.4_20140910">kggseq</requirement>\n+ <requirement type="package" version="0.7_20150118">kggseq</requirement>\n </requirements>\n <command>\n java -jar \\$KGGSEQ_JAR_PATH/kggseq.jar\n@@ -19,49 +19,37 @@\n --db-gene $db_gene\n $composite_subject_id\n \n-## Variant filters\n+## Variant and genotype filters\n $pass_variant_only\n-#if str($variant_filters.variant_filters_select) == "yes"\n- --seq-qual $variant_filters.seq_qual\n- --seq-mq $variant_filters.seq_mq\n- --seq-sb $variant_filters.seq_sb\n- --seq-fs $variant_filters.seq_fs\n- --min-heta $variant_filters.min_heta\n- --min-homa $variant_filters.min_homa\n- --min-hetu $variant_filters.min_hetu\n- --min-homu $variant_filters.min_homu\n- --min-obsa $variant_filters.min_obsa\n- --min-obsu $variant_filters.min_obsu\n- --min-obs $variant_filters.min_obs\n- #if str($variant_filters.hwe_control)\n- --hwe-control $variant_filters.hwe_control\n- #end if\n- #if str($variant_filters.hwe_case)\n- --hwe-case $variant_filters.hwe_case\n+#if str($variant_genotype_filters.variant_genotype_filters_select) == "yes"\n+ --seq-qual $variant_genotype_filters.seq_qual\n+ --seq-mq $variant_genotype_filters.seq_mq\n+ --seq-sb $variant_genotype_filters.seq_sb\n+ --seq-fs $variant_genotype_filters.seq_fs\n+ --min-heta $variant_genotype_filters.min_heta\n+ --min-homa $variant_genotype_filters.min_homa\n+ --min-hetu $variant_genotype_filters.min_hetu\n+ --min-homu $variant_genotype_filters.min_homu\n+ --min-obsa $variant_genotype_filters.min_obsa\n+ --min-obsu $variant_genotype_filters.min_obsu\n+ --min-obs $variant_genotype_filters.min_obs\n+ #if str($variant_genotype_filters.hwe_control)\n+ --hwe-control $variant_genotype_filters.hwe_control\n #end if\n- #if str($variant_filters.hwe_all)\n- --hwe-all $variant_filters.hwe_all\n+ #if str($variant_genotype_filters.hwe_case)\n+ --hwe-case $variant_genotype_filters.hwe_case\n+ #end if\n+ #if str($variant_genotype_filters.hwe_all)\n+ --hwe-all $variant_genotype_filters.hwe_all\n #end if\n+ --gty-qual $variant_genotype_filters.gty_qual\n+ --gty-dp $variant_genotype_filters.gty_dp\n+ --gty-sec-pl $variant_genotype_filters.gty_sec_pl\n+ --gty-af-ref $variant_genotype_filters.gty_af_ref\n+ --gty-af-het $variant_genotype_filters.gty_af_het\n+ --gty-af-alt $variant_genotype_filters.gty_af_alt\n #else\n- --seq-qual 0\n- --seq-mq 0\n-#end if\n-\n-## Genotype filters\n-#if str($genotype_filters.genotype_filters_select) == "yes"\n- --gty-qual $genotype_filters.gty_qual\n- --gty-dp $genotype_filters.gty_dp\n- --gty-sec-pl $genotype_filters.gty_sec_pl\n- --gty-af-ref $genotype_filters.gty_af_ref\n- --gty-af-het $genotype_filters.gty_af_het\n- --gty-af-alt $genotype_filters.gty_af_alt\n-#else\n- --gty-qual 0\n- --gty-dp 0\n- --gty-sec-pl 0\n- --gty-af-ref 1\n- --gty-af-het 0\n- --gty-af-alt 0\n+ --no-qc\n #end if\n \n ## Genetic inheritance\n@@ -75,6 +63,19 @@\n #end if\n #end if\n \n+## Homozygosity - IBS - IBD filters\n+#if str($hom_ibs_ibd_filters.hom_ibs_ibd_filters_select) == "yes"\n+ #if str($hom_ibs_ibd_filters.homozygosity_case_filter)\n+ --homozygosity-case-filter $hom_ibs_ibd_filters.homozygosity_case_filter\n+ #end if\n+ #if str($hom_ibs_ibd_filters.ibs_case_filter)\n+ --ibs-case-filter $hom_ibs_ibd_filters.ibs_case_filter\n+ #end if\n+ #if str($hom_ibs_ibd_filters.ibd_annot) != \'None\'\n+ --ibd-annot $hom_ibs_ibd_filters.ibd_annot\n+ #end if\n+#end if\n+\n ## Gene feature filters\n #if str($gene_feature_filters.gene_feature_filters_select) == "yes" and $gene_feature_filters.gene_features\n --gene-feature-in $gene_feature_filters.gene_features\n@@ -120,6 +121,9 @@\n \n ## Add annotations\n #if str($add_annotations.add_annotations_select) == "yes"\n+ #if str($add_annotations.o_flanking_'..b' <option value="1kg201204">1KG 201204: 1000 Genomes Project 2012 April release</option>\n+ <option value="1kgafr201204">1KG 201204 AFR: 1000 Genomes Project 2012 April release - African</option>\n+ <option value="1kgeur201204">1KG 201204 EUR: 1000 Genomes Project 2012 April release - European</option>\n+ <option value="1kgamr201204">1KG 201204 AMR: 1000 Genomes Project 2012 April release - Mixed American</option>\n+ <option value="1kgasn201204">1KG 201204 ASN: 1000 Genomes Project 2012 April release - Asian</option>\n+ <option value="ESP6500AA" selected="true">ESP6500AA: African American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option>\n+ <option value="ESP6500EA" selected="true">ESP6500EA: European American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option>\n+ <option value="dbsnp141" selected="true">dnSNP 141</option>\n+ <option value="dbsnp138">dbSNP 138</option>\n+ <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>\n+ <option value="dbsnp137">dbSNP 137</option>\n+ <option value="dbsnp135">dbSNP 135</option>\n+ <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>\n </param>\n <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" />\n </when>\n@@ -314,7 +330,7 @@\n <option value="no" selected="true">No</option>\n </param>\n <when value="yes">\n- <param name="filter_nondisease_variant" type="boolean" truevalue="--filter-nondisease-variant" falsevalue="" checked="true" label="Filter out variants predicted to be non-disease causal (--filter-nondisease-variant)" />\n+ <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)" />\n <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)" />\n </when>\n <when value="no" />\n@@ -327,10 +343,11 @@\n <option value="no" selected="true">No</option>\n </param>\n <when value="yes">\n+ <param name="o_flanking_seq" type="integer" value="" label="Size in bp of flanking sequence to extract (--o-flanking-seq)" />\n <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" />\n <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" />\n <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" />\n- <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with:">\n+ <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with">\n <option value="--pubmed-mining">The cytogenetic position of each variant (--pubmed-mining)</option>\n <option value="--pubmed-mining-gene">The gene in which each variant is located (--pubmed-mining-gene)</option>\n </param>\n'

diff -r d388273fb83f -r e9758eee6697 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Sep 12 21:40:16 2014 -0400
+++ b/tool_dependencies.xml Tue Apr 28 04:42:14 2015 -0400

@@ -1,11 +1,12 @@
<?xml version="1.0"?>
<tool_dependency>
-  <package name="kggseq" version="0.4_20140910">
+  <package name="kggseq" version="0.7_20150118">
     <install version="1.0">
       <actions>
-        <action type="download_by_url" target_filename="kggseq_archive-0.4_20140910.tar.gz">https://github.com/nsoranzo/kggseq_archive/archive/v0.4_20140910.tar.gz</action>
+        <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="shell_command">touch test.vcf</action>
-        <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter hg19_1kg201305,hg19_1kg201204,hg19_ESP6500AA,hg19_ESP6500EA,hg19_dbsnp141,hg19_dbsnp138,hg19_dbsnp137 --genome-annot --db-gene refgene,gencode,knowngene --db-score dbnsfp --superdup-annot --vcf-file 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>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>