1
+ − 1 <tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.2">
0
+ − 2 <description></description>
+ − 3 <requirements>
1
+ − 4 <requirement type="package" version="0.7_20150118">kggseq</requirement>
0
+ − 5 </requirements>
+ − 6 <command>
+ − 7 java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
+ − 8 ## Environmental settings
+ − 9 --buildver hg19
+ − 10 --resource \$KGGSEQ_JAR_PATH/resources
+ − 11 --no-lib-check
+ − 12 --no-resource-check
+ − 13 --no-progress-check
+ − 14 --out results
+ − 15 --o-vcf
+ − 16
+ − 17 --vcf-file $inputFile
+ − 18 --ped-file $pedFile
+ − 19 --db-gene $db_gene
+ − 20 $composite_subject_id
+ − 21
1
+ − 22 ## Variant and genotype filters
0
+ − 23 $pass_variant_only
1
+ − 24 #if str($variant_genotype_filters.variant_genotype_filters_select) == "yes"
+ − 25 --seq-qual $variant_genotype_filters.seq_qual
+ − 26 --seq-mq $variant_genotype_filters.seq_mq
+ − 27 --seq-sb $variant_genotype_filters.seq_sb
+ − 28 --seq-fs $variant_genotype_filters.seq_fs
+ − 29 --min-heta $variant_genotype_filters.min_heta
+ − 30 --min-homa $variant_genotype_filters.min_homa
+ − 31 --min-hetu $variant_genotype_filters.min_hetu
+ − 32 --min-homu $variant_genotype_filters.min_homu
+ − 33 --min-obsa $variant_genotype_filters.min_obsa
+ − 34 --min-obsu $variant_genotype_filters.min_obsu
+ − 35 --min-obs $variant_genotype_filters.min_obs
+ − 36 #if str($variant_genotype_filters.hwe_control)
+ − 37 --hwe-control $variant_genotype_filters.hwe_control
0
+ − 38 #end if
1
+ − 39 #if str($variant_genotype_filters.hwe_case)
+ − 40 --hwe-case $variant_genotype_filters.hwe_case
+ − 41 #end if
+ − 42 #if str($variant_genotype_filters.hwe_all)
+ − 43 --hwe-all $variant_genotype_filters.hwe_all
0
+ − 44 #end if
1
+ − 45 --gty-qual $variant_genotype_filters.gty_qual
+ − 46 --gty-dp $variant_genotype_filters.gty_dp
+ − 47 --gty-sec-pl $variant_genotype_filters.gty_sec_pl
+ − 48 --gty-af-ref $variant_genotype_filters.gty_af_ref
+ − 49 --gty-af-het $variant_genotype_filters.gty_af_het
+ − 50 --gty-af-alt $variant_genotype_filters.gty_af_alt
0
+ − 51 #else
1
+ − 52 --no-qc
0
+ − 53 #end if
+ − 54
+ − 55 ## Genetic inheritance
+ − 56 #if str($genetic_filters.genetic_filters_select) == "yes"
+ − 57 #if str($genetic_filters.genetic_model.genetic_model_select) == "yes"
+ − 58 #if $genetic_filters.genetic_model.custom_genetic_params
+ − 59 --genotype-filter $genetic_filters.genetic_model.custom_genetic_params
+ − 60 #end if
+ − 61 #else
+ − 62 $genetic_filters.genetic_model.suggested_genetic_params
+ − 63 #end if
+ − 64 #end if
+ − 65
1
+ − 66 ## Homozygosity - IBS - IBD filters
+ − 67 #if str($hom_ibs_ibd_filters.hom_ibs_ibd_filters_select) == "yes"
+ − 68 #if str($hom_ibs_ibd_filters.homozygosity_case_filter)
+ − 69 --homozygosity-case-filter $hom_ibs_ibd_filters.homozygosity_case_filter
+ − 70 #end if
+ − 71 #if str($hom_ibs_ibd_filters.ibs_case_filter)
+ − 72 --ibs-case-filter $hom_ibs_ibd_filters.ibs_case_filter
+ − 73 #end if
+ − 74 #if str($hom_ibs_ibd_filters.ibd_annot) != 'None'
+ − 75 --ibd-annot $hom_ibs_ibd_filters.ibd_annot
+ − 76 #end if
+ − 77 #end if
+ − 78
0
+ − 79 ## Gene feature filters
+ − 80 #if str($gene_feature_filters.gene_feature_filters_select) == "yes" and $gene_feature_filters.gene_features
+ − 81 --gene-feature-in $gene_feature_filters.gene_features
+ − 82 --splicing $gene_feature_filters.splicing
+ − 83 --neargene $gene_feature_filters.neargene
+ − 84 #end if
+ − 85
+ − 86 ## Common variants filters
+ − 87 #if str($allele_freq_filters.allele_freq_filters_select) == "yes"
+ − 88 #if $allele_freq_filters.allele_freq_db
+ − 89 --db-filter $allele_freq_filters.allele_freq_db
+ − 90 #end if
+ − 91 --rare-allele-freq $allele_freq_filters.rare_allele_freq
+ − 92 #end if
+ − 93
+ − 94 ## Genomic regions filters
+ − 95 #if str($genomic_region_filters.genomic_region_filters_select) == "yes"
+ − 96 $genomic_region_filters.ignore_indel_or_snv
+ − 97 #if $genomic_region_filters.regions_in
+ − 98 --regions-in "$genomic_region_filters.regions_in"
+ − 99 #end if
+ − 100 #if $genomic_region_filters.regions_out
+ − 101 --regions-out "$genomic_region_filters.regions_out"
+ − 102 #end if
+ − 103 #if $genomic_region_filters.genes_in
+ − 104 --genes-in "$genomic_region_filters.genes_in"
+ − 105 #end if
+ − 106 #if $genomic_region_filters.genes_out
+ − 107 --genes-out "$genomic_region_filters.genes_out"
+ − 108 #end if
+ − 109 $genomic_region_filters.superdup
+ − 110 #if str($genomic_region_filters.gene_var_filter)
+ − 111 --gene-var-filter $genomic_region_filters.gene_var_filter
+ − 112 #end if
+ − 113 #end if
+ − 114
+ − 115 ## Predicted impact filters
+ − 116 #if str($impact_filters.impact_filters_select) == "yes"
+ − 117 --db-score dbnsfp
+ − 118 $impact_filters.filter_nondisease_variant
+ − 119 $impact_filters.mendel_causing
+ − 120 #end if
+ − 121
+ − 122 ## Add annotations
+ − 123 #if str($add_annotations.add_annotations_select) == "yes"
1
+ − 124 #if str($add_annotations.o_flanking_seq)
+ − 125 --o-flanking-seq $add_annotations.o_flanking_seq
+ − 126 #end if
0
+ − 127 $add_annotations.genome_annotation
+ − 128 $add_annotations.omim_annotation
+ − 129 $add_annotations.cosmic_annotation
+ − 130 #if $add_annotations.pubmed_mining_gene
+ − 131 $add_annotations.pubmed_type "$add_annotations.pubmed_mining_gene"
+ − 132 #end if
+ − 133 #if str($add_annotations.shared_genes.shared_genes_select) == "yes"
+ − 134 --ppi-annot string
+ − 135 --candi-file $add_annotations.shared_genes.candi_file
+ − 136 --ppi-depth $add_annotations.shared_genes.ppi_depth
+ − 137 --pathway-annot $add_annotations.shared_genes.pathway_annot
+ − 138 #end if
+ − 139 #end if
+ − 140 > $logFile
+ − 141 </command>
+ − 142 <inputs>
+ − 143 <param name="inputFile" type="data" format="vcf" label="VCF Variant file (--vcf-file)" help="Coordinates must refer to hg19" />
+ − 144 <param name="pedFile" type="data" format="tabular" label="Pedigree (--ped-file)" />
1
+ − 145 <param name="composite_subject_id" type="boolean" truevalue="--composite-subject-id" falsevalue="" checked="false" label="Composite subject ID (--composite-subject-id)" />
0
+ − 146 <param name="db_gene" type="select" display="checkboxes" multiple="true" label="Database(s) to annotate and filter variants (--db-gene)">
+ − 147 <option value="refgene" selected="true">refgene: The RefGene database compiled by UCSC from hg19 refGene. Note: RefSeq has NO mitochondria gene definition</option>
1
+ − 148 <option value="gencode">gencode: The GENCODE gene sets. Note: GENCODE contains similar number of coding genes but more transcripts than RefGene. It HAS the mitochondria gene definition</option>
0
+ − 149 <option value="knowngene">knowngene: The UCSC knonwGene datasase compiled by UCSC from hg19 knownGene</option>
1
+ − 150 <option value="ensembl">ensembl: The Ensembl gene datasase compiled by UCSC from hg19 ensGene</option>
0
+ − 151 <validator type="no_options" message="Select at least one database" />
+ − 152 </param>
+ − 153 <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" />
+ − 154
1
+ − 155 <!-- Variant and genotype quality control -->
+ − 156 <conditional name="variant_genotype_filters">
+ − 157 <param name="variant_genotype_filters_select" type="select" label="Specify variant and genotype quality filters?">
0
+ − 158 <option value="yes">Yes</option>
+ − 159 <option value="no" selected="true">No</option>
+ − 160 </param>
+ − 161 <when value="yes">
+ − 162 <param name="seq_qual" type="integer" value="50" label="Minimum overall Phred-scaled sequencing quality score for the variant (--seq-qual)" />
+ − 163 <param name="seq_mq" type="integer" value="20" label="Minimum overall Phred-scaled mapping quality score for the variant (--seq-mq)" />
+ − 164 <param name="seq_sb" type="float" value="-10" label="Maximal overall strand bias score for the variant (--seq-sb)" />
+ − 165 <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)" />
1
+ − 166 <param name="min_heta" type="integer" value="0" label="Minimal observed number of heterozygote genotypes in cases (the affected) (--min-heta)" />
+ − 167 <param name="min_homa" type="integer" value="0" label="Minimal observed number of alternate homozygote genotypes in cases (the affected) (--min-homa)" />
+ − 168 <param name="min_hetu" type="integer" value="0" label="Minimal observed number of heterozygote genotypes in controls (the unaffected) (--min-hetu)" />
+ − 169 <param name="min_homu" type="integer" value="0" label="Minimal observed number of alternate homozygote genotypes in controls (the unaffected) (--min-homu)" />
+ − 170 <param name="min_obsa" type="integer" value="0" label="Minimal observed number of non-missing genotypes in cases (the affected) (--min-obsa)" />
+ − 171 <param name="min_obsu" type="integer" value="0" label="Minimal observed number of non-missing genotypes in controls (the unaffected) (--min-obsu)" />
+ − 172 <param name="min_obs" type="integer" value="1" label="Minimal observed number of non-missing genotypes in all samples (--min-obs)" />
0
+ − 173 <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)" />
+ − 174 <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)" />
+ − 175 <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)" />
+ − 176 <param name="gty_qual" type="integer" value="10" label="Minimum Phred-scaled genotyping quality (--gty-qual)" />
+ − 177 <param name="gty_dp" type="integer" value="4" label="Minimal read depth per genotype (--gty-dp)" />
+ − 178 <param name="gty_sec_pl" type="integer" value="20" label="Minimal value for second smallest normalized Phred-scaled genotype quality (--gty-sec-pl)" />
+ − 179 <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)" />
+ − 180 <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)" />
+ − 181 <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)" />
+ − 182 </when>
+ − 183 <when value="no" />
+ − 184 </conditional>
+ − 185
+ − 186 <!-- Genetic inheritance -->
+ − 187 <conditional name="genetic_filters">
+ − 188 <param name="genetic_filters_select" type="select" label="Specify genetic inheritance?">
+ − 189 <option value="yes">Yes</option>
+ − 190 <option value="no" selected="true">No</option>
+ − 191 </param>
+ − 192 <when value="yes">
+ − 193 <conditional name="genetic_model">
+ − 194 <param name="genetic_model_select" type="select" label="Specify advanced settings for genetic inheritance?">
+ − 195 <option value="yes">Yes</option>
+ − 196 <option value="no" selected="true">No</option>
+ − 197 </param>
+ − 198 <!-- Custom genetic filters -->
+ − 199 <when value="yes">
+ − 200 <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">
+ − 201 <option value="1">Exclude variants at which affected subjects have heterozygous genotypes (1)</option>
+ − 202 <option value="2">Exclude variants at which both affected and unaffected subjects have the same homozygous genotypes (2)</option>
+ − 203 <option value="3">Exclude variants at which affected subjects have reference homozygous genotypes (3)</option>
+ − 204 <option value="4">Exclude variants at which both affected and unaffected subjects have the same heterozygous genotypes (4)</option>
+ − 205 <option value="5">Exclude variants at which affected subjects have alternative homozygous genotypes (5)</option>
+ − 206 <option value="6">Exclude variants at which affected family members have NO shared alleles (6)</option>
+ − 207 <option value="7">ONLY include variants at which an offspring has one or two non-inherited alleles (7)</option>
+ − 208 </param>
+ − 209 </when>
+ − 210 <!-- Suggested genetic filters -->
+ − 211 <when value="no">
+ − 212 <param name="suggested_genetic_params" type="select" display="radio" label="Select genetic inheritance">
+ − 213 <option value="--genotype-filter 1,2,3">Recessive (--genotype-filter 1,2,3)</option>
+ − 214 <option value="--double-hit-gene-trio-filter" selected="true">Recessive and compound-heterozygous (--double-hit-gene-trio-filter)</option>
+ − 215 <option value="--double-hit-gene-phased-filter">Recessive and compound-heterozygous with phased samples (--double-hit-gene-phased-filter)</option>
+ − 216 <option value="--genotype-filter 2,3,4,5">Dominant (--genotype-filter 2,3,4,5)</option>
+ − 217 <option value="--genotype-filter 7">De novo mutation (--genotype-filter 7)</option>
+ − 218 <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>
+ − 219 </param>
+ − 220 </when>
+ − 221 </conditional>
+ − 222 </when>
+ − 223 <when value="no" />
+ − 224 </conditional>
+ − 225
1
+ − 226 <!-- Homozygosity filtering -->
+ − 227 <conditional name="hom_ibs_ibd_filters">
+ − 228 <param name="hom_ibs_ibd_filters_select" type="select" label="Specify homozygosity filters?">
+ − 229 <option value="yes">Yes</option>
+ − 230 <option value="no" selected="true">No</option>
+ − 231 </param>
+ − 232 <when value="yes">
+ − 233 <param name="homozygosity_case_filter" type="integer" value="" optional="true" label="Filter by Runs of Homozygosity (ROH) (--homozygosity-case-filter)" help="Minimal length (in kb) of consecutive homozygous genotype for each interesting variant" />
+ − 234 <param name="ibs_case_filter" type="integer" value="" optional="true" label="Filter by Identical by State (IBS) (--ibs-case-filter)" help="Minimal length (in kb) of the region in which there is at least one allele identical among all cases" />
+ − 235 <param name="ibd_annot" type="data" format="txt,tabular,bed" optional="true" label="Add Identical by Descent (IBD) annotation (--ibd-annot)" help="File with IBD or significant linkage regions. Variants within these regions will be highlighted. Note: title line CHR START END is needed" />
+ − 236 </when>
+ − 237 <when value="no" />
+ − 238 </conditional>
+ − 239
0
+ − 240 <!-- Gene feature filtering -->
+ − 241 <conditional name="gene_feature_filters">
+ − 242 <param name="gene_feature_filters_select" type="select" label="Specify gene feature filters?">
+ − 243 <option value="yes">Yes</option>
+ − 244 <option value="no" selected="true">No</option>
+ − 245 </param>
+ − 246 <when value="yes">
+ − 247 <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">
+ − 248 <option value="0" selected="true">Frame-shift</option>
+ − 249 <option value="1" selected="true">Loss of amino acids</option>
+ − 250 <option value="2" selected="true">Loss of stop codon (TAG, TAA, TGA)</option>
+ − 251 <option value="3" selected="true">Gain of stop codon (TAG, TAA, TGA)</option>
+ − 252 <option value="4" selected="true">Missense</option>
+ − 253 <option value="5" selected="true">Splicing</option>
+ − 254 <option value="6">Synonymous</option>
+ − 255 <option value="7">Exonic</option>
+ − 256 <option value="8">5-UTR</option>
+ − 257 <option value="9">3-UTR</option>
+ − 258 <option value="10">Intronic</option>
+ − 259 <option value="11">Upstream of transcription start site</option>
+ − 260 <option value="12">Downstream of transcription end site</option>
+ − 261 <option value="13">ncRNA</option>
+ − 262 <option value="14">Intergenic</option>
1
+ − 263 <option value="15">Monomorphic</option>
+ − 264 <option value="16">Unknown</option>
0
+ − 265 </param>
+ − 266 <param name="splicing" type="integer" value="2" label="Window size in base-pair around the splicing junction to flag the variant as splicing (--splicing)" />
1
+ − 267 <param name="neargene" type="integer" value="1000" label="Size in base-pair of region upstream and downstream (--neargene)" />
0
+ − 268 </when>
+ − 269 <when value="no" />
+ − 270 </conditional>
+ − 271
+ − 272 <!-- Allele frequency filtering -->
+ − 273 <conditional name="allele_freq_filters">
1
+ − 274 <param name="allele_freq_filters_select" type="select" label="Specify filters by allele frequency?">
0
+ − 275 <option value="yes">Yes</option>
+ − 276 <option value="no" selected="true">No</option>
+ − 277 </param>
+ − 278 <when value="yes">
+ − 279 <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)">
1
+ − 280 <option value="1kg201305" selected="true">1KG 201305: 1000 Genomes Project 2013 May release</option>
+ − 281 <option value="1kg201204">1KG 201204: 1000 Genomes Project 2012 April release</option>
+ − 282 <option value="1kgafr201204">1KG 201204 AFR: 1000 Genomes Project 2012 April release - African</option>
+ − 283 <option value="1kgeur201204">1KG 201204 EUR: 1000 Genomes Project 2012 April release - European</option>
+ − 284 <option value="1kgamr201204">1KG 201204 AMR: 1000 Genomes Project 2012 April release - Mixed American</option>
+ − 285 <option value="1kgasn201204">1KG 201204 ASN: 1000 Genomes Project 2012 April release - Asian</option>
+ − 286 <option value="ESP6500AA" selected="true">ESP6500AA: African American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option>
+ − 287 <option value="ESP6500EA" selected="true">ESP6500EA: European American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option>
+ − 288 <option value="dbsnp141" selected="true">dnSNP 141</option>
+ − 289 <option value="dbsnp138">dbSNP 138</option>
+ − 290 <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>
+ − 291 <option value="dbsnp137">dbSNP 137</option>
+ − 292 <option value="dbsnp135">dbSNP 135</option>
+ − 293 <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>
0
+ − 294 </param>
+ − 295 <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" />
+ − 296 </when>
+ − 297 <when value="no" />
+ − 298 </conditional>
+ − 299
+ − 300 <!-- Variant type, region and gene filtering -->
+ − 301 <conditional name="genomic_region_filters">
+ − 302 <param name="genomic_region_filters_select" type="select" label="Specify variant type, region and gene filtering?">
+ − 303 <option value="yes">Yes</option>
+ − 304 <option value="no" selected="true">No</option>
+ − 305 </param>
+ − 306 <when value="yes">
+ − 307 <param name="ignore_indel_or_snv" type="select" label="Ignore indels or SNVs?">
+ − 308 <option value="" selected="true">No</option>
+ − 309 <option value="--ignore-indel">Ignore insertion and deletion sequence variants (indels) (--ignore-indel)</option>
+ − 310 <option value="--ignore-snv">Ignore single nucleotide variants (SNVs) (--ignore-snv)</option>
+ − 311 </param>
+ − 312 <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" />
+ − 313 <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" />
+ − 314 <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" />
+ − 315 <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" />
+ − 316 <param name="superdup" type="select" label="Annotate or filter out variants in super duplicate regions?" help="As defined in genomicSuperDups dataset from UCSC">
+ − 317 <option value="" selected="true">No</option>
+ − 318 <option value="--superdup-annot">Annotate variants in super duplicate regions (--superdup-annot)</option>
+ − 319 <option value="--superdup-filter">Filter out variants in super duplicate regions (--superdup-filter)</option>
+ − 320 </param>
+ − 321 <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. " />
+ − 322 </when>
+ − 323 <when value="no" />
+ − 324 </conditional>
+ − 325
+ − 326 <!-- Predicted impact filtering -->
+ − 327 <conditional name="impact_filters">
+ − 328 <param name="impact_filters_select" type="select" label="Specify functional impact filters?">
+ − 329 <option value="yes">Yes</option>
+ − 330 <option value="no" selected="true">No</option>
+ − 331 </param>
+ − 332 <when value="yes">
1
+ − 333 <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)" />
0
+ − 334 <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)" />
+ − 335 </when>
+ − 336 <when value="no" />
+ − 337 </conditional>
+ − 338
+ − 339 <!-- Annotations -->
+ − 340 <conditional name="add_annotations">
+ − 341 <param name="add_annotations_select" type="select" label="Add annotations?">
+ − 342 <option value="yes">Yes</option>
+ − 343 <option value="no" selected="true">No</option>
+ − 344 </param>
+ − 345 <when value="yes">
1
+ − 346 <param name="o_flanking_seq" type="integer" value="" label="Size in bp of flanking sequence to extract (--o-flanking-seq)" />
0
+ − 347 <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" />
+ − 348 <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" />
+ − 349 <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" />
1
+ − 350 <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with">
0
+ − 351 <option value="--pubmed-mining">The cytogenetic position of each variant (--pubmed-mining)</option>
+ − 352 <option value="--pubmed-mining-gene">The gene in which each variant is located (--pubmed-mining-gene)</option>
+ − 353 </param>
+ − 354 <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" />
+ − 355 <!-- Shared protein-protein interactions and pathways -->
+ − 356 <conditional name="shared_genes">
+ − 357 <param name="shared_genes_select" type="select" label="Add annotations for shared interactions/pathways?">
+ − 358 <option value="yes">Yes</option>
+ − 359 <option value="no" selected="true">No</option>
+ − 360 </param>
+ − 361 <when value="yes">
+ − 362 <param name="candi_file" type="data" format="txt,tabular" label="List of candidate genes of interest (--candi-file)" />
+ − 363 <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)" />
+ − 364 <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">
+ − 365 <option value="cura" selected="true">Curated gene sets (4850)</option>
+ − 366 <option value="cano">Canonical pathways (1452)</option>
+ − 367 <option value="onco">Oncogenic signatures (189)</option>
+ − 368 <option value="cmop">Computational gene sets (858)</option>
+ − 369 <option value="onto">Gene Ontology gene sets (1454)</option>
+ − 370 </param>
+ − 371 </when>
+ − 372 <when value="no" />
+ − 373 </conditional>
+ − 374 </when>
+ − 375 <when value="no" />
+ − 376 </conditional>
+ − 377 </inputs>
+ − 378 <outputs>
+ − 379 <data name="outVcf" format="vcf" label="${tool.name} on ${on_string}: VCF" from_work_dir="results.flt.vcf" />
+ − 380 <data name="outTabular" format="tabular" label="${tool.name} on ${on_string}: tabular" from_work_dir="results.flt.txt" />
+ − 381 <data name="outDoubleHitTriosGty" format="tabular" label="${tool.name} on ${on_string}: double-hit genotypes" from_work_dir="results.doublehit.gene.trios.flt.gty.txt">
+ − 382 <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-trio-filter"</filter>
+ − 383 </data>
+ − 384 <data name="outDoubleHitTriosCount" format="tabular" label="${tool.name} on ${on_string}: double-hit counts" from_work_dir="results.doublehit.gene.trios.flt.count.txt">
+ − 385 <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-trio-filter"</filter>
+ − 386 </data>
+ − 387 <data name="outDoubleHitPhasedGty" format="tabular" label="${tool.name} on ${on_string}: double-hit phased genotypes" from_work_dir="results.doublehit.gene.phased.flt.gty.txt">
+ − 388 <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-phased-filter"</filter>
+ − 389 </data>
+ − 390 <data name="outDoubleHitPhasedCount" format="tabular" label="${tool.name} on ${on_string}: double-hit phased counts" from_work_dir="results.doublehit.gene.phased.flt.count.txt">
+ − 391 <filter>genetic_filters['genetic_filters_select'] == "yes" and genetic_filters['genetic_model']['genetic_model_select'] == "no" and genetic_filters['genetic_model']['suggested_genetic_params'] == "--double-hit-gene-phased-filter"</filter>
+ − 392 </data>
+ − 393 <data name="logFile" format="txt" label="${tool.name} on ${on_string}: log" />
+ − 394 </outputs>
+ − 395 <help>
+ − 396 **What it does**
+ − 397
+ − 398 This tool uses `KGGSeq`_ to filter and prioritize genetic variants from sequencing data.
+ − 399
+ − 400 **License and citation**
+ − 401
+ − 402 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
+ − 403
+ − 404 .. _CRS4 Srl.: http://www.crs4.it/
+ − 405 .. _MIT license: http://opensource.org/licenses/MIT
+ − 406
+ − 407 You can use this tool only if you agree to the license terms of: `KGGSeq`_.
+ − 408
+ − 409 .. _KGGSeq: http://statgenpro.psychiatry.hku.hk/limx/kggseq/
+ − 410
+ − 411 If you use this tool, please cite:
+ − 412
+ − 413 - |Cuccuru2014|_
+ − 414 - |Li2012|_
+ − 415 - |Li2013|_.
+ − 416
+ − 417 .. |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
+ − 418 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
+ − 419 .. |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
+ − 420 .. _Li2012: http://nar.oxfordjournals.org/content/40/7/e53
+ − 421 .. |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
+ − 422 .. _Li2013: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003143
+ − 423 </help>
+ − 424 </tool>
