Mercurial > repos > crs4 > kggseq_variant_selection
changeset 3:c758125c56d8 draft
Update to KggSeq release 0.8 (23/Apr./2015)
| author | crs4 |
|---|---|
| date | Mon, 25 May 2015 18:01:25 -0400 |
| parents | e1a21c2f4997 |
| children | a13b8ff61c6c |
| files | kggseq_variant_selection.xml tool_dependencies.xml |
| diffstat | 2 files changed, 21 insertions(+), 20 deletions(-) [+] |
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--- 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>