# HG changeset patch
# User crs4
# Date 1410572416 14400
# Node ID d388273fb83f1a7319e6ad4ebc3a8201e64bcc34

Uploaded

diff -r 000000000000 -r d388273fb83f COPYING
--- /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.
diff -r 000000000000 -r d388273fb83f kggseq_variant_selection.xml
--- /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
+&gt; $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 &lt;= 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 &lt;= 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 &lt;= 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 &gt;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>
diff -r 000000000000 -r d388273fb83f tool_dependencies.xml
--- /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>