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comparison kggseq_variant_selection.xml @ 1:e9758eee6697 draft

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Update to KggSeq v0.7_20150118
author crs4
date Tue, 28 Apr 2015 04:42:14 -0400
parents d388273fb83f
children e1a21c2f4997
comparison
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0:d388273fb83f 1:e9758eee6697
1 <tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.1"> 1 <tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.4_20140910">kggseq</requirement> 4 <requirement type="package" version="0.7_20150118">kggseq</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 java -jar \$KGGSEQ_JAR_PATH/kggseq.jar 7 java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
8 ## Environmental settings 8 ## Environmental settings
9 --buildver hg19 9 --buildver hg19
17 --vcf-file $inputFile 17 --vcf-file $inputFile
18 --ped-file $pedFile 18 --ped-file $pedFile
19 --db-gene $db_gene 19 --db-gene $db_gene
20 $composite_subject_id 20 $composite_subject_id
21 21
22 ## Variant filters 22 ## Variant and genotype filters
23 $pass_variant_only 23 $pass_variant_only
24 #if str($variant_filters.variant_filters_select) == "yes" 24 #if str($variant_genotype_filters.variant_genotype_filters_select) == "yes"
25 --seq-qual $variant_filters.seq_qual 25 --seq-qual $variant_genotype_filters.seq_qual
26 --seq-mq $variant_filters.seq_mq 26 --seq-mq $variant_genotype_filters.seq_mq
27 --seq-sb $variant_filters.seq_sb 27 --seq-sb $variant_genotype_filters.seq_sb
28 --seq-fs $variant_filters.seq_fs 28 --seq-fs $variant_genotype_filters.seq_fs
29 --min-heta $variant_filters.min_heta 29 --min-heta $variant_genotype_filters.min_heta
30 --min-homa $variant_filters.min_homa 30 --min-homa $variant_genotype_filters.min_homa
31 --min-hetu $variant_filters.min_hetu 31 --min-hetu $variant_genotype_filters.min_hetu
32 --min-homu $variant_filters.min_homu 32 --min-homu $variant_genotype_filters.min_homu
33 --min-obsa $variant_filters.min_obsa 33 --min-obsa $variant_genotype_filters.min_obsa
34 --min-obsu $variant_filters.min_obsu 34 --min-obsu $variant_genotype_filters.min_obsu
35 --min-obs $variant_filters.min_obs 35 --min-obs $variant_genotype_filters.min_obs
36 #if str($variant_filters.hwe_control) 36 #if str($variant_genotype_filters.hwe_control)
37 --hwe-control $variant_filters.hwe_control 37 --hwe-control $variant_genotype_filters.hwe_control
38 #end if 38 #end if
39 #if str($variant_filters.hwe_case) 39 #if str($variant_genotype_filters.hwe_case)
40 --hwe-case $variant_filters.hwe_case 40 --hwe-case $variant_genotype_filters.hwe_case
41 #end if 41 #end if
42 #if str($variant_filters.hwe_all) 42 #if str($variant_genotype_filters.hwe_all)
43 --hwe-all $variant_filters.hwe_all 43 --hwe-all $variant_genotype_filters.hwe_all
44 #end if 44 #end if
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 $variant_genotype_filters.gty_af_alt
45 #else 51 #else
46 --seq-qual 0 52 --no-qc
47 --seq-mq 0
48 #end if
49
50 ## Genotype filters
51 #if str($genotype_filters.genotype_filters_select) == "yes"
52 --gty-qual $genotype_filters.gty_qual
53 --gty-dp $genotype_filters.gty_dp
54 --gty-sec-pl $genotype_filters.gty_sec_pl
55 --gty-af-ref $genotype_filters.gty_af_ref
56 --gty-af-het $genotype_filters.gty_af_het
57 --gty-af-alt $genotype_filters.gty_af_alt
58 #else
59 --gty-qual 0
60 --gty-dp 0
61 --gty-sec-pl 0
62 --gty-af-ref 1
63 --gty-af-het 0
64 --gty-af-alt 0
65 #end if 53 #end if
66 54
67 ## Genetic inheritance 55 ## Genetic inheritance
68 #if str($genetic_filters.genetic_filters_select) == "yes" 56 #if str($genetic_filters.genetic_filters_select) == "yes"
69 #if str($genetic_filters.genetic_model.genetic_model_select) == "yes" 57 #if str($genetic_filters.genetic_model.genetic_model_select) == "yes"
73 #else 61 #else
74 $genetic_filters.genetic_model.suggested_genetic_params 62 $genetic_filters.genetic_model.suggested_genetic_params
75 #end if 63 #end if
76 #end if 64 #end if
77 65
66 ## Homozygosity - IBS - IBD filters
67 #if str($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 $hom_ibs_ibd_filters.ibd_annot
76 #end if
77 #end if
78
78 ## Gene feature filters 79 ## Gene feature filters
79 #if str($gene_feature_filters.gene_feature_filters_select) == "yes" and $gene_feature_filters.gene_features 80 #if str($gene_feature_filters.gene_feature_filters_select) == "yes" and $gene_feature_filters.gene_features
80 --gene-feature-in $gene_feature_filters.gene_features 81 --gene-feature-in $gene_feature_filters.gene_features
81 --splicing $gene_feature_filters.splicing 82 --splicing $gene_feature_filters.splicing
82 --neargene $gene_feature_filters.neargene 83 --neargene $gene_feature_filters.neargene
118 $impact_filters.mendel_causing 119 $impact_filters.mendel_causing
119 #end if 120 #end if
120 121
121 ## Add annotations 122 ## Add annotations
122 #if str($add_annotations.add_annotations_select) == "yes" 123 #if str($add_annotations.add_annotations_select) == "yes"
124 #if str($add_annotations.o_flanking_seq)
125 --o-flanking-seq $add_annotations.o_flanking_seq
126 #end if
123 $add_annotations.genome_annotation 127 $add_annotations.genome_annotation
124 $add_annotations.omim_annotation 128 $add_annotations.omim_annotation
125 $add_annotations.cosmic_annotation 129 $add_annotations.cosmic_annotation
126 #if $add_annotations.pubmed_mining_gene 130 #if $add_annotations.pubmed_mining_gene
127 $add_annotations.pubmed_type "$add_annotations.pubmed_mining_gene" 131 $add_annotations.pubmed_type "$add_annotations.pubmed_mining_gene"
136 &gt; $logFile 140 &gt; $logFile
137 </command> 141 </command>
138 <inputs> 142 <inputs>
139 <param name="inputFile" type="data" format="vcf" label="VCF Variant file (--vcf-file)" help="Coordinates must refer to hg19" /> 143 <param name="inputFile" type="data" format="vcf" label="VCF Variant file (--vcf-file)" help="Coordinates must refer to hg19" />
140 <param name="pedFile" type="data" format="tabular" label="Pedigree (--ped-file)" /> 144 <param name="pedFile" type="data" format="tabular" label="Pedigree (--ped-file)" />
145 <param name="composite_subject_id" type="boolean" truevalue="--composite-subject-id" falsevalue="" checked="false" label="Composite subject ID (--composite-subject-id)" />
141 <param name="db_gene" type="select" display="checkboxes" multiple="true" label="Database(s) to annotate and filter variants (--db-gene)"> 146 <param name="db_gene" type="select" display="checkboxes" multiple="true" label="Database(s) to annotate and filter variants (--db-gene)">
142 <option value="refgene" selected="true">refgene: The RefGene database compiled by UCSC from hg19 refGene. Note: RefSeq has NO mitochondria gene definition</option> 147 <option value="refgene" selected="true">refgene: The RefGene database compiled by UCSC from hg19 refGene. Note: RefSeq has NO mitochondria gene definition</option>
143 <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> 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>
144 <option value="knowngene">knowngene: The UCSC knonwGene datasase compiled by UCSC from hg19 knownGene</option> 149 <option value="knowngene">knowngene: The UCSC knonwGene datasase compiled by UCSC from hg19 knownGene</option>
150 <option value="ensembl">ensembl: The Ensembl gene datasase compiled by UCSC from hg19 ensGene</option>
145 <validator type="no_options" message="Select at least one database" /> 151 <validator type="no_options" message="Select at least one database" />
146 </param> 152 </param>
147 <param name="composite_subject_id" type="boolean" truevalue="--composite-subject-id" falsevalue="" checked="false" label="Composite subject ID (--composite-subject-id)" />
148 <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" /> 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" />
149 154
150 <!-- Variant quality control --> 155 <!-- Variant and genotype quality control -->
151 <conditional name="variant_filters"> 156 <conditional name="variant_genotype_filters">
152 <param name="variant_filters_select" type="select" label="Specify variant quality filters?"> 157 <param name="variant_genotype_filters_select" type="select" label="Specify variant and genotype quality filters?">
153 <option value="yes">Yes</option> 158 <option value="yes">Yes</option>
154 <option value="no" selected="true">No</option> 159 <option value="no" selected="true">No</option>
155 </param> 160 </param>
156 <when value="yes"> 161 <when value="yes">
157 <param name="seq_qual" type="integer" value="50" label="Minimum overall Phred-scaled sequencing quality score for the variant (--seq-qual)" /> 162 <param name="seq_qual" type="integer" value="50" label="Minimum overall Phred-scaled sequencing quality score for the variant (--seq-qual)" />
158 <param name="seq_mq" type="integer" value="20" label="Minimum overall Phred-scaled mapping quality score for the variant (--seq-mq)" /> 163 <param name="seq_mq" type="integer" value="20" label="Minimum overall Phred-scaled mapping quality score for the variant (--seq-mq)" />
159 <param name="seq_sb" type="float" value="-10" label="Maximal overall strand bias score for the variant (--seq-sb)" /> 164 <param name="seq_sb" type="float" value="-10" label="Maximal overall strand bias score for the variant (--seq-sb)" />
160 <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)" /> 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)" />
161 <param name="min_heta" type="integer" value="1" label="Minimal observed number of heterozygote genotypes in cases (the affected) (--min-heta)" /> 166 <param name="min_heta" type="integer" value="0" label="Minimal observed number of heterozygote genotypes in cases (the affected) (--min-heta)" />
162 <param name="min_homa" type="integer" value="1" label="Minimal observed number of alternate homozygote genotypes in cases (the affected) (--min-homa)" /> 167 <param name="min_homa" type="integer" value="0" label="Minimal observed number of alternate homozygote genotypes in cases (the affected) (--min-homa)" />
163 <param name="min_hetu" type="integer" value="1" label="Minimal observed number of heterozygote genotypes in controls (the unaffected) (--min-hetu)" /> 168 <param name="min_hetu" type="integer" value="0" label="Minimal observed number of heterozygote genotypes in controls (the unaffected) (--min-hetu)" />
164 <param name="min_homu" type="integer" value="1" label="Minimal observed number of alternate homozygote genotypes in controls (the unaffected) (--min-homu)" /> 169 <param name="min_homu" type="integer" value="0" label="Minimal observed number of alternate homozygote genotypes in controls (the unaffected) (--min-homu)" />
165 <param name="min_obsa" type="integer" value="1" label="Minimal observed number of non-missing genotypes in cases (the affected) (--min-obsa)" /> 170 <param name="min_obsa" type="integer" value="0" label="Minimal observed number of non-missing genotypes in cases (the affected) (--min-obsa)" />
166 <param name="min_obsu" type="integer" value="1" label="Minimal observed number of non-missing genotypes in controls (the unaffected) (--min-obsu)" /> 171 <param name="min_obsu" type="integer" value="0" label="Minimal observed number of non-missing genotypes in controls (the unaffected) (--min-obsu)" />
167 <param name="min_obs" type="integer" value="2" label="Minimal observed number of non-missing genotypes in all samples (--min-obs)" /> 172 <param name="min_obs" type="integer" value="1" label="Minimal observed number of non-missing genotypes in all samples (--min-obs)" />
168 <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)" /> 173 <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)" />
169 <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)" /> 174 <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)" />
170 <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)" /> 175 <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)" />
171 </when>
172 <when value="no" />
173 </conditional>
174
175 <!-- Genotype quality control -->
176 <conditional name="genotype_filters">
177 <param name="genotype_filters_select" type="select" label="Specify genotype quality filters?">
178 <option value="yes">Yes</option>
179 <option value="no" selected="true">No</option>
180 </param>
181 <when value="yes">
182 <param name="gty_qual" type="integer" value="10" label="Minimum Phred-scaled genotyping quality (--gty-qual)" /> 176 <param name="gty_qual" type="integer" value="10" label="Minimum Phred-scaled genotyping quality (--gty-qual)" />
183 <param name="gty_dp" type="integer" value="4" label="Minimal read depth per genotype (--gty-dp)" /> 177 <param name="gty_dp" type="integer" value="4" label="Minimal read depth per genotype (--gty-dp)" />
184 <param name="gty_sec_pl" type="integer" value="20" label="Minimal value for second smallest normalized Phred-scaled genotype quality (--gty-sec-pl)" /> 178 <param name="gty_sec_pl" type="integer" value="20" label="Minimal value for second smallest normalized Phred-scaled genotype quality (--gty-sec-pl)" />
185 <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)" /> 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)" />
186 <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)" /> 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)" />
227 </conditional> 221 </conditional>
228 </when> 222 </when>
229 <when value="no" /> 223 <when value="no" />
230 </conditional> 224 </conditional>
231 225
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
232 <!-- Gene feature filtering --> 240 <!-- Gene feature filtering -->
233 <conditional name="gene_feature_filters"> 241 <conditional name="gene_feature_filters">
234 <param name="gene_feature_filters_select" type="select" label="Specify gene feature filters?"> 242 <param name="gene_feature_filters_select" type="select" label="Specify gene feature filters?">
235 <option value="yes">Yes</option> 243 <option value="yes">Yes</option>
236 <option value="no" selected="true">No</option> 244 <option value="no" selected="true">No</option>
250 <option value="10">Intronic</option> 258 <option value="10">Intronic</option>
251 <option value="11">Upstream of transcription start site</option> 259 <option value="11">Upstream of transcription start site</option>
252 <option value="12">Downstream of transcription end site</option> 260 <option value="12">Downstream of transcription end site</option>
253 <option value="13">ncRNA</option> 261 <option value="13">ncRNA</option>
254 <option value="14">Intergenic</option> 262 <option value="14">Intergenic</option>
255 <option value="15">Unknown</option> 263 <option value="15">Monomorphic</option>
264 <option value="16">Unknown</option>
256 </param> 265 </param>
257 <param name="splicing" type="integer" value="2" label="Window size in base-pair around the splicing junction to flag the variant as splicing (--splicing)" /> 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)" />
258 <param name="neargene" type="integer" value="1000" label="Size of region upstream and downstream (--neargene)" /> 267 <param name="neargene" type="integer" value="1000" label="Size in base-pair of region upstream and downstream (--neargene)" />
259 </when> 268 </when>
260 <when value="no" /> 269 <when value="no" />
261 </conditional> 270 </conditional>
262 271
263 <!-- Allele frequency filtering --> 272 <!-- Allele frequency filtering -->
264 <conditional name="allele_freq_filters"> 273 <conditional name="allele_freq_filters">
265 <param name="allele_freq_filters_select" type="select" label="Specify common variants filters?"> 274 <param name="allele_freq_filters_select" type="select" label="Specify filters by allele frequency?">
266 <option value="yes">Yes</option> 275 <option value="yes">Yes</option>
267 <option value="no" selected="true">No</option> 276 <option value="no" selected="true">No</option>
268 </param> 277 </param>
269 <when value="yes"> 278 <when value="yes">
270 <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)"> 279 <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)">
271 <option value="hg19_1kg201305" selected="true">hg19_1kg201305: 1000 Genomes Project 2013 May release</option> 280 <option value="1kg201305" selected="true">1KG 201305: 1000 Genomes Project 2013 May release</option>
272 <option value="hg19_1kg201204">hg19_1kg201204: 1000 Genomes Project 2012 April release</option> 281 <option value="1kg201204">1KG 201204: 1000 Genomes Project 2012 April release</option>
273 <option value="hg19_ESP6500AA" selected="true">hg19_ESP6500AA: African American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option> 282 <option value="1kgafr201204">1KG 201204 AFR: 1000 Genomes Project 2012 April release - African</option>
274 <option value="hg19_ESP6500EA" selected="true">hg19_ESP6500EA: European American dataset from NHLBI GO Exome Sequencing Project (ESP6500)</option> 283 <option value="1kgeur201204">1KG 201204 EUR: 1000 Genomes Project 2012 April release - European</option>
275 <option value="hg19_dbsnp141" selected="true">hg19_dbsnp141: dbSNP version 141</option> 284 <option value="1kgamr201204">1KG 201204 AMR: 1000 Genomes Project 2012 April release - Mixed American</option>
276 <option value="hg19_dbsnp138">hg19_dbsnp138: dbSNP version 138</option> 285 <option value="1kgasn201204">1KG 201204 ASN: 1000 Genomes Project 2012 April release - Asian</option>
277 <option value="hg19_dbsnp137">hg19_dbsnp137: dbSNP version 137</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>
278 </param> 294 </param>
279 <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" /> 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 &gt;1 to only annotate MAF, without filtering" />
280 </when> 296 </when>
281 <when value="no" /> 297 <when value="no" />
282 </conditional> 298 </conditional>
312 <param name="impact_filters_select" type="select" label="Specify functional impact filters?"> 328 <param name="impact_filters_select" type="select" label="Specify functional impact filters?">
313 <option value="yes">Yes</option> 329 <option value="yes">Yes</option>
314 <option value="no" selected="true">No</option> 330 <option value="no" selected="true">No</option>
315 </param> 331 </param>
316 <when value="yes"> 332 <when value="yes">
317 <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)" /> 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)" />
318 <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)" /> 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)" />
319 </when> 335 </when>
320 <when value="no" /> 336 <when value="no" />
321 </conditional> 337 </conditional>
322 338
325 <param name="add_annotations_select" type="select" label="Add annotations?"> 341 <param name="add_annotations_select" type="select" label="Add annotations?">
326 <option value="yes">Yes</option> 342 <option value="yes">Yes</option>
327 <option value="no" selected="true">No</option> 343 <option value="no" selected="true">No</option>
328 </param> 344 </param>
329 <when value="yes"> 345 <when value="yes">
346 <param name="o_flanking_seq" type="integer" value="" label="Size in bp of flanking sequence to extract (--o-flanking-seq)" />
330 <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" /> 347 <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" />
331 <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" /> 348 <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" />
332 <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" /> 349 <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" />
333 <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with:"> 350 <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with">
334 <option value="--pubmed-mining">The cytogenetic position of each variant (--pubmed-mining)</option> 351 <option value="--pubmed-mining">The cytogenetic position of each variant (--pubmed-mining)</option>
335 <option value="--pubmed-mining-gene">The gene in which each variant is located (--pubmed-mining-gene)</option> 352 <option value="--pubmed-mining-gene">The gene in which each variant is located (--pubmed-mining-gene)</option>
336 </param> 353 </param>
337 <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" /> 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" />
338 <!-- Shared protein-protein interactions and pathways --> 355 <!-- Shared protein-protein interactions and pathways -->