Mercurial > repos > crs4 > kggseq_variant_selection
changeset 0:d388273fb83f draft
Uploaded
| author | crs4 |
|---|---|
| date | Fri, 12 Sep 2014 21:40:16 -0400 |
| parents | |
| children | e9758eee6697 |
| files | COPYING kggseq_variant_selection.xml tool_dependencies.xml |
| diffstat | 3 files changed, 449 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Sep 12 21:40:16 2014 -0400 @@ -0,0 +1,23 @@ +Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ +Created by: +Paolo Uva <paolo.uva@crs4.it> +Nicola Soranzo <nicola.soranzo@crs4.it> + +Permission is hereby granted, free of charge, to any person obtaining a +copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be included +in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. +IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY +CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, +TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE +SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kggseq_variant_selection.xml Fri Sep 12 21:40:16 2014 -0400 @@ -0,0 +1,407 @@ +<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.1"> + <description></description> + <requirements> + <requirement type="package" version="0.4_20140910">kggseq</requirement> + </requirements> + <command> +java -jar \$KGGSEQ_JAR_PATH/kggseq.jar +## Environmental settings +--buildver hg19 +--resource \$KGGSEQ_JAR_PATH/resources +--no-lib-check +--no-resource-check +--no-progress-check +--out results +--o-vcf + +--vcf-file $inputFile +--ped-file $pedFile +--db-gene $db_gene +$composite_subject_id + +## Variant filters +$pass_variant_only +#if str($variant_filters.variant_filters_select) == "yes" + --seq-qual $variant_filters.seq_qual + --seq-mq $variant_filters.seq_mq + --seq-sb $variant_filters.seq_sb + --seq-fs $variant_filters.seq_fs + --min-heta $variant_filters.min_heta + --min-homa $variant_filters.min_homa + --min-hetu $variant_filters.min_hetu + --min-homu $variant_filters.min_homu + --min-obsa $variant_filters.min_obsa + --min-obsu $variant_filters.min_obsu + --min-obs $variant_filters.min_obs + #if str($variant_filters.hwe_control) + --hwe-control $variant_filters.hwe_control + #end if + #if str($variant_filters.hwe_case) + --hwe-case $variant_filters.hwe_case + #end if + #if str($variant_filters.hwe_all) + --hwe-all $variant_filters.hwe_all + #end if +#else + --seq-qual 0 + --seq-mq 0 +#end if + +## Genotype filters +#if str($genotype_filters.genotype_filters_select) == "yes" + --gty-qual $genotype_filters.gty_qual + --gty-dp $genotype_filters.gty_dp + --gty-sec-pl $genotype_filters.gty_sec_pl + --gty-af-ref $genotype_filters.gty_af_ref + --gty-af-het $genotype_filters.gty_af_het + --gty-af-alt $genotype_filters.gty_af_alt +#else + --gty-qual 0 + --gty-dp 0 + --gty-sec-pl 0 + --gty-af-ref 1 + --gty-af-het 0 + --gty-af-alt 0 +#end if + +## Genetic inheritance +#if str($genetic_filters.genetic_filters_select) == "yes" + #if str($genetic_filters.genetic_model.genetic_model_select) == "yes" + #if $genetic_filters.genetic_model.custom_genetic_params + --genotype-filter $genetic_filters.genetic_model.custom_genetic_params + #end if + #else + $genetic_filters.genetic_model.suggested_genetic_params + #end if +#end if + +## Gene feature filters +#if str($gene_feature_filters.gene_feature_filters_select) == "yes" and $gene_feature_filters.gene_features + --gene-feature-in $gene_feature_filters.gene_features + --splicing $gene_feature_filters.splicing + --neargene $gene_feature_filters.neargene +#end if + +## Common variants filters +#if str($allele_freq_filters.allele_freq_filters_select) == "yes" + #if $allele_freq_filters.allele_freq_db + --db-filter $allele_freq_filters.allele_freq_db + #end if + --rare-allele-freq $allele_freq_filters.rare_allele_freq +#end if + +## Genomic regions filters +#if str($genomic_region_filters.genomic_region_filters_select) == "yes" + $genomic_region_filters.ignore_indel_or_snv + #if $genomic_region_filters.regions_in + --regions-in "$genomic_region_filters.regions_in" + #end if + #if $genomic_region_filters.regions_out + --regions-out "$genomic_region_filters.regions_out" + #end if + #if $genomic_region_filters.genes_in + --genes-in "$genomic_region_filters.genes_in" + #end if + #if $genomic_region_filters.genes_out + --genes-out "$genomic_region_filters.genes_out" + #end if + $genomic_region_filters.superdup + #if str($genomic_region_filters.gene_var_filter) + --gene-var-filter $genomic_region_filters.gene_var_filter + #end if +#end if + +## Predicted impact filters +#if str($impact_filters.impact_filters_select) == "yes" + --db-score dbnsfp + $impact_filters.filter_nondisease_variant + $impact_filters.mendel_causing +#end if + +## Add annotations +#if str($add_annotations.add_annotations_select) == "yes" + $add_annotations.genome_annotation + $add_annotations.omim_annotation + $add_annotations.cosmic_annotation + #if $add_annotations.pubmed_mining_gene + $add_annotations.pubmed_type "$add_annotations.pubmed_mining_gene" + #end if + #if str($add_annotations.shared_genes.shared_genes_select) == "yes" + --ppi-annot string + --candi-file $add_annotations.shared_genes.candi_file + --ppi-depth $add_annotations.shared_genes.ppi_depth + --pathway-annot $add_annotations.shared_genes.pathway_annot + #end if +#end if +> $logFile + </command> + <inputs> + <param name="inputFile" type="data" format="vcf" label="VCF Variant file (--vcf-file)" help="Coordinates must refer to hg19" /> + <param name="pedFile" type="data" format="tabular" label="Pedigree (--ped-file)" /> + <param name="db_gene" type="select" display="checkboxes" multiple="true" label="Database(s) to annotate and filter variants (--db-gene)"> + <option value="refgene" selected="true">refgene: The RefGene database compiled by UCSC from hg19 refGene. Note: RefSeq has NO mitochondria gene definition</option> + <option value="gencode">gencode: The GENCODE gene sets. Note: GECODE contains similar number of coding genes but more transcripts than RefGene. It HAS the mitochondria gene definition</option> + <option value="knowngene">knowngene: The UCSC knonwGene datasase compiled by UCSC from hg19 knownGene</option> + <validator type="no_options" message="Select at least one database" /> + </param> + <param name="composite_subject_id" type="boolean" truevalue="--composite-subject-id" falsevalue="" checked="false" label="Composite subject ID (--composite-subject-id)" /> + <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 quality control --> + <conditional name="variant_filters"> + <param name="variant_filters_select" type="select" label="Specify variant quality filters?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <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)" /> + <param name="seq_fs" type="integer" value="60" label="Maximal overall strand bias Phred-scaled p-value (using Fisher's exact test) for the variant (--seq-fs)" /> + <param name="min_heta" type="integer" value="1" label="Minimal observed number of heterozygote genotypes in cases (the affected) (--min-heta)" /> + <param name="min_homa" type="integer" value="1" label="Minimal observed number of alternate homozygote genotypes in cases (the affected) (--min-homa)" /> + <param name="min_hetu" type="integer" value="1" label="Minimal observed number of heterozygote genotypes in controls (the unaffected) (--min-hetu)" /> + <param name="min_homu" type="integer" value="1" label="Minimal observed number of alternate homozygote genotypes in controls (the unaffected) (--min-homu)" /> + <param name="min_obsa" type="integer" value="1" label="Minimal observed number of non-missing genotypes in cases (the affected) (--min-obsa)" /> + <param name="min_obsu" type="integer" value="1" label="Minimal observed number of non-missing genotypes in controls (the unaffected) (--min-obsu)" /> + <param name="min_obs" type="integer" value="2" label="Minimal observed number of non-missing genotypes in all samples (--min-obs)" /> + <param name="hwe_control" type="float" value="" optional="true" label="Exclude variants in controls with the Hardy-Weinberg test p-value <= this value (--hwe-control)" /> + <param name="hwe_case" type="float" value="" optional="true" label="Exclude variants in cases with the Hardy-Weinberg test p-value <= this value (--hwe-case)" /> + <param name="hwe_all" type="float" value="" optional="true" label="Exclude variants in all subjects with the Hardy-Weinberg test p-value <= this value (--hwe-all)" /> + </when> + <when value="no" /> + </conditional> + + <!-- Genotype quality control --> + <conditional name="genotype_filters"> + <param name="genotype_filters_select" type="select" label="Specify genotype quality filters?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="gty_qual" type="integer" value="10" label="Minimum Phred-scaled genotyping quality (--gty-qual)" /> + <param name="gty_dp" type="integer" value="4" label="Minimal read depth per genotype (--gty-dp)" /> + <param name="gty_sec_pl" type="integer" value="20" label="Minimal value for second smallest normalized Phred-scaled genotype quality (--gty-sec-pl)" /> + <param name="gty_af_ref" type="float" value="0.05" label="Maximal fraction of reads carrying alternative allele at a reference allele homozygous genotype (--gty-af-ref)" /> + <param name="gty_af_het" type="float" value="0.25" label="Minimal fraction of reads carrying alternative allele at a heterozygous genotype (--gty-af-het)" /> + <param name="gty_af_alt" type="float" value="0.5" label="Minimal fraction of reads carrying alternative allele at a alternative allele homozygous genotype (--gty-af-alt)" /> + </when> + <when value="no" /> + </conditional> + + <!-- Genetic inheritance --> + <conditional name="genetic_filters"> + <param name="genetic_filters_select" type="select" label="Specify genetic inheritance?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <conditional name="genetic_model"> + <param name="genetic_model_select" type="select" label="Specify advanced settings for genetic inheritance?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <!-- Custom genetic filters --> + <when value="yes"> + <param name="custom_genetic_params" type="select" display="checkboxes" multiple="true" label="Select genetic inheritance (advanced) (--genotype-filter)" help="Multiple filtration codes have logical OR relationship"> + <option value="1">Exclude variants at which affected subjects have heterozygous genotypes (1)</option> + <option value="2">Exclude variants at which both affected and unaffected subjects have the same homozygous genotypes (2)</option> + <option value="3">Exclude variants at which affected subjects have reference homozygous genotypes (3)</option> + <option value="4">Exclude variants at which both affected and unaffected subjects have the same heterozygous genotypes (4)</option> + <option value="5">Exclude variants at which affected subjects have alternative homozygous genotypes (5)</option> + <option value="6">Exclude variants at which affected family members have NO shared alleles (6)</option> + <option value="7">ONLY include variants at which an offspring has one or two non-inherited alleles (7)</option> + </param> + </when> + <!-- Suggested genetic filters --> + <when value="no"> + <param name="suggested_genetic_params" type="select" display="radio" label="Select genetic inheritance"> + <option value="--genotype-filter 1,2,3">Recessive (--genotype-filter 1,2,3)</option> + <option value="--double-hit-gene-trio-filter" selected="true">Recessive and compound-heterozygous (--double-hit-gene-trio-filter)</option> + <option value="--double-hit-gene-phased-filter">Recessive and compound-heterozygous with phased samples (--double-hit-gene-phased-filter)</option> + <option value="--genotype-filter 2,3,4,5">Dominant (--genotype-filter 2,3,4,5)</option> + <option value="--genotype-filter 7">De novo mutation (--genotype-filter 7)</option> + <option value="--unique-gene-filter">Only genes on which EVERY affected subject has at least one case-unique alternative allele, but these alleles may be from different variants (--unique-gene-filter)</option> + </param> + </when> + </conditional> + </when> + <when value="no" /> + </conditional> + + <!-- Gene feature filtering --> + <conditional name="gene_feature_filters"> + <param name="gene_feature_filters_select" type="select" label="Specify gene feature filters?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <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="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">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 of region upstream and downstream (--neargene)" /> + </when> + <when value="no" /> + </conditional> + + <!-- Allele frequency filtering --> + <conditional name="allele_freq_filters"> + <param name="allele_freq_filters_select" type="select" label="Specify common variants filters?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)"> + <option value="hg19_1kg201305" selected="true">hg19_1kg201305: 1000 Genomes Project 2013 May release</option> + <option value="hg19_1kg201204">hg19_1kg201204: 1000 Genomes Project 2012 April release</option> + <option value="hg19_ESP6500AA" selected="true">hg19_ESP6500AA: African American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option> + <option value="hg19_ESP6500EA" selected="true">hg19_ESP6500EA: European American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option> + <option value="hg19_dbsnp141" selected="true">hg19_dbsnp141: dbSNP version 141</option> + <option value="hg19_dbsnp138">hg19_dbsnp138: dbSNP version 138</option> + <option value="hg19_dbsnp137">hg19_dbsnp137: dbSNP version 137</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> + <when value="no" /> + </conditional> + + <!-- Variant type, region and gene filtering --> + <conditional name="genomic_region_filters"> + <param name="genomic_region_filters_select" type="select" label="Specify variant type, region and gene filtering?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="ignore_indel_or_snv" type="select" label="Ignore indels or SNVs?"> + <option value="" selected="true">No</option> + <option value="--ignore-indel">Ignore insertion and deletion sequence variants (indels) (--ignore-indel)</option> + <option value="--ignore-snv">Ignore single nucleotide variants (SNVs) (--ignore-snv)</option> + </param> + <param name="regions_in" type="text" label="Keep only variants within some genomic regions (--regions-in)" help="A comma-separated list of genomic regions, e.g. chrX,chrY:1-1000" /> + <param name="regions_out" type="text" label="Ignore variants within some genomic regions (--regions-out)" help="A comma-separated list of genomic regions, e.g. chrX,chrY:1-1000" /> + <param name="genes_in" type="text" label="Keep only variants within some genes (--genes-in)" help="A comma-separated list of gene symbols, e.g. TCF4,CNNM2,ANK3" /> + <param name="genes_out" type="text" label="Ignore variants within some genes (--genes-out)" help="A comma-separated list of gene symbols, e.g. TCF4,CNNM2,ANK3" /> + <param name="superdup" type="select" label="Annotate or filter out variants in super duplicate regions?" help="As defined in genomicSuperDups dataset from UCSC"> + <option value="" selected="true">No</option> + <option value="--superdup-annot">Annotate variants in super duplicate regions (--superdup-annot)</option> + <option value="--superdup-filter">Filter out variants in super duplicate regions (--superdup-filter)</option> + </param> + <param name="gene_var_filter" type="integer" value="" optional="true" label="Filter out genes with at least this number of putative pathogenic variants (--gene-var-filter)" help="As a rule of thumb, it is safe to set a cutoff of 4 or more. " /> + </when> + <when value="no" /> + </conditional> + + <!-- Predicted impact filtering --> + <conditional name="impact_filters"> + <param name="impact_filters_select" type="select" label="Specify functional impact filters?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <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)" /> + <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)" /> + </when> + <when value="no" /> + </conditional> + + <!-- Annotations --> + <conditional name="add_annotations"> + <param name="add_annotations_select" type="select" label="Add annotations?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" /> + <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" /> + <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" /> + <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with:"> + <option value="--pubmed-mining">The cytogenetic position of each variant (--pubmed-mining)</option> + <option value="--pubmed-mining-gene">The gene in which each variant is located (--pubmed-mining-gene)</option> + </param> + <param name="pubmed_mining_gene" type="text" label="Text mining in PubMed: search term(s) of interest (e.g. disease name)" help="A comma-separated list of search terms, each composed by plus-separated words, e.g. spinocerebellar+ataxia,other+search+term. If empty, no search will be performed" /> + <!-- Shared protein-protein interactions and pathways --> + <conditional name="shared_genes"> + <param name="shared_genes_select" type="select" label="Add annotations for shared interactions/pathways?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="candi_file" type="data" format="txt,tabular" label="List of candidate genes of interest (--candi-file)" /> + <param name="ppi_depth" type="integer" value="1" label="Maximum distance of a protein-protein interaction (PPI) between candidate genes and genes containing the variants (--ppi-depth)" /> + <param name="pathway_annot" type="select" label="Select databases for the identification of shared pathways between candidate genes and genes containing the variants (--pathway-annot)" help="Gene sets are extracted from MSigDB"> + <option value="cura" selected="true">Curated gene sets (4850)</option> + <option value="cano">Canonical pathways (1452)</option> + <option value="onco">Oncogenic signatures (189)</option> + <option value="cmop">Computational gene sets (858)</option> + <option value="onto">Gene Ontology gene sets (1454)</option> + </param> + </when> + <when value="no" /> + </conditional> + </when> + <when value="no" /> + </conditional> + </inputs> + <outputs> + <data name="outVcf" format="vcf" label="${tool.name} on ${on_string}: VCF" from_work_dir="results.flt.vcf" /> + <data name="outTabular" format="tabular" label="${tool.name} on ${on_string}: tabular" from_work_dir="results.flt.txt" /> + <data name="outDoubleHitTriosGty" format="tabular" label="${tool.name} on ${on_string}: double-hit genotypes" from_work_dir="results.doublehit.gene.trios.flt.gty.txt"> + <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-trio-filter"</filter> + </data> + <data name="outDoubleHitTriosCount" format="tabular" label="${tool.name} on ${on_string}: double-hit counts" from_work_dir="results.doublehit.gene.trios.flt.count.txt"> + <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-trio-filter"</filter> + </data> + <data name="outDoubleHitPhasedGty" format="tabular" label="${tool.name} on ${on_string}: double-hit phased genotypes" from_work_dir="results.doublehit.gene.phased.flt.gty.txt"> + <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-phased-filter"</filter> + </data> + <data name="outDoubleHitPhasedCount" format="tabular" label="${tool.name} on ${on_string}: double-hit phased counts" from_work_dir="results.doublehit.gene.phased.flt.count.txt"> + <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-phased-filter"</filter> + </data> + <data name="logFile" format="txt" label="${tool.name} on ${on_string}: log" /> + </outputs> + <help> +**What it does** + +This tool uses `KGGSeq`_ to filter and prioritize genetic variants from sequencing data. + +**License and citation** + +This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _MIT license: http://opensource.org/licenses/MIT + +You can use this tool only if you agree to the license terms of: `KGGSeq`_. + +.. _KGGSeq: http://statgenpro.psychiatry.hku.hk/limx/kggseq/ + +If you use this tool, please cite: + +- |Cuccuru2014|_ +- |Li2012|_ +- |Li2013|_. + +.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929 +.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 +.. |Li2012| replace:: Li, M.-X., *et al.* (2012) A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. *Nucleic Acids Res.* 40(7), e53 +.. _Li2012: http://nar.oxfordjournals.org/content/40/7/e53 +.. |Li2013| replace:: Li, M.-X., *et al.* (2013) Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies. *PLoS Genet.* 9(1), e1003143 +.. _Li2013: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003143 + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 12 21:40:16 2014 -0400 @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="kggseq" version="0.4_20140910"> + <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="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="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="KGGSEQ_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency>