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comparison kggseq_variant_selection.xml @ 4:a13b8ff61c6c draft

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planemo upload
author crs4
date Thu, 04 Aug 2016 04:40:06 -0400
parents c758125c56d8
children dc45e612bc47
comparison
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3:c758125c56d8 4:a13b8ff61c6c
1 <tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.3"> 1 <tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.4">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.8_20150423 ">kggseq</requirement> 4 <requirement type="package" version="1.0_0_20160412">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
11 --no-lib-check 11 --no-lib-check
12 --no-resource-check 12 --no-resource-check
13 --no-progress-check 13 --no-progress-check
14 --out results 14 --out results
15 --o-vcf 15 --o-vcf
16 --no-gz
16 17
17 --vcf-file $inputFile 18 --vcf-file $inputFile
18 --ped-file $pedFile 19 --ped-file $pedFile
19 --db-gene $db_gene 20 --db-gene $db_gene
20 $composite_subject_id 21 $composite_subject_id
124 #if str($add_annotations.o_flanking_seq) 125 #if str($add_annotations.o_flanking_seq)
125 --o-flanking-seq $add_annotations.o_flanking_seq 126 --o-flanking-seq $add_annotations.o_flanking_seq
126 #end if 127 #end if
127 $add_annotations.genome_annotation 128 $add_annotations.genome_annotation
128 $add_annotations.omim_annotation 129 $add_annotations.omim_annotation
129 $add_annotations.cosmic_annotation 130 $add_annotations.cosmic_annotation
131 $add_annotations.scsnv_annotation
132 $add_annotations.dgv_cnv_annotation
133 $add_annotations.superdup_annotation
134 $add_annotations.mouse_pheno_annotation
135 $add_annotations.zebrafish_pheno_annotation
136 $add_annotations.ddd_annotation
137 $add_annotations.patho_gene_predict_annotation
130 #if $add_annotations.pubmed_mining_gene 138 #if $add_annotations.pubmed_mining_gene
131 $add_annotations.pubmed_type "$add_annotations.pubmed_mining_gene" 139 --phenotype-term "$add_annotations.pubmed_mining_gene" --pubmed-mining
132 #end if 140 #end if
133 #if str($add_annotations.shared_genes.shared_genes_select) == "yes" 141 #if str($add_annotations.shared_genes.shared_genes_select) == "yes"
134 --ppi-annot string 142 --ppi-annot string
135 --candi-file $add_annotations.shared_genes.candi_file 143 --candi-file $add_annotations.shared_genes.candi_file
136 --ppi-depth $add_annotations.shared_genes.ppi_depth 144 --ppi-depth $add_annotations.shared_genes.ppi_depth
275 <param name="allele_freq_filters_select" type="select" label="Specify filters by allele frequency?"> 283 <param name="allele_freq_filters_select" type="select" label="Specify filters by allele frequency?">
276 <option value="yes">Yes</option> 284 <option value="yes">Yes</option>
277 <option value="no" selected="true">No</option> 285 <option value="no" selected="true">No</option>
278 </param> 286 </param>
279 <when value="yes"> 287 <when value="yes">
280 <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)"> 288 <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)">
289 <option value="1kgeur201305">1KG EUR 201305: 495 subjects in the EUR panel of 1000 Genomes Project release in 2013 May (around 24.0 million sequence variants)</option>
290 <option value="1kgeas201305">1KG EAS 201305: 496 subjects in the EAS panel of 1000 Genomes Project release in 2013 May (around 23.5 million sequence variants)</option>
291 <option value="1kgafr201305">1KG AFR 201305: 645 subjects in the AFR panel of 1000 Genomes Project release in 2013 May (around 41.7 million sequence variants)</option>
292 <option value="1kgsas201305">1KG SAS 201305: 485 subjects in the SAS panel of 1000 Genomes Project release in 2013 May (around 26.7 million sequence variants)</option>
293 <option value="1kgamr201305">1KG AMR 201305: 346 subjects in the AMR panel of 1000 Genomes Project release in 2013 May (around 28.2 million sequence variants)</option>
281 <option value="1kg201305" selected="true">1KG 201305: 1000 Genomes Project 2013 May release</option> 294 <option value="1kg201305" selected="true">1KG 201305: 1000 Genomes Project 2013 May release</option>
282 <option value="1kg201204">1KG 201204: 1000 Genomes Project 2012 April release</option> 295 <option value="1kg201204">1KG 201204: 1000 Genomes Project 2012 April release</option>
283 <option value="1kgafr201204">1KG 201204 AFR: 1000 Genomes Project 2012 April release - African</option> 296 <option value="1kgafr201204">1KG 201204 AFR: 1000 Genomes Project 2012 April release - African</option>
284 <option value="1kgeur201204">1KG 201204 EUR: 1000 Genomes Project 2012 April release - European</option> 297 <option value="1kgeur201204">1KG 201204 EUR: 1000 Genomes Project 2012 April release - European</option>
285 <option value="1kgamr201204">1KG 201204 AMR: 1000 Genomes Project 2012 April release - Mixed American</option> 298 <option value="1kgamr201204">1KG 201204 AMR: 1000 Genomes Project 2012 April release - Mixed American</option>
345 </param> 358 </param>
346 <when value="yes"> 359 <when value="yes">
347 <param name="o_flanking_seq" type="integer" value="" optional="true" label="Size in bp of flanking sequence to extract (--o-flanking-seq)" /> 360 <param name="o_flanking_seq" type="integer" value="" optional="true" label="Size in bp of flanking sequence to extract (--o-flanking-seq)" />
348 <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" /> 361 <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" />
349 <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" /> 362 <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" />
350 <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" /> 363 <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" />
351 <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with"> 364 <param name="scsnv_annotation" type="boolean" truevalue="--scsnv-annot" falsevalue="" checked="true" label="Potential of altering splicing (--scsnv-annot)" />
352 <option value="--pubmed-mining">The cytogenetic position of each variant (--pubmed-mining)</option> 365 <param name="dgv_cnv_annotation" type="boolean" truevalue="--dgv-cnv-annot" falsevalue="" checked="true" label="Map a variant against known structure variation (--dgv-cnv-annot)" />
353 <option value="--pubmed-mining-gene">The gene in which each variant is located (--pubmed-mining-gene)</option> 366 <param name="superdup_annotation" type="boolean" truevalue="--superdup-annot" falsevalue="" checked="true" label="Mark the variants in the super duplicate regions (--superdup-annot)" />
354 </param> 367 <param name="mouse_pheno_annotation" type="boolean" truevalue="--mouse-pheno" falsevalue="" checked="true" label="Annotate the genes with known mouse phenotypes as reference (--mouse-pheno)" />
368 <param name="zebrafish_pheno_annotation" type="boolean" truevalue="--zebrafish-pheno" falsevalue="" checked="true" label="Annotate the genes with known zebrafish phenotypes as reference (--zebrafish-pheno)" />
369 <param name="ddd_annotation" type="boolean" truevalue="--ddd-annot" falsevalue="" checked="true" label="Annotate by disease names in Deciphering Developmental Disorders (DDD) study (--ddd-annot)" />
370 <param name="patho_gene_predict_annotation" type="boolean" truevalue="--patho-gene-predict" falsevalue="" checked="true" label="Predict genes’ pathogenicity (--patho-gene-predict)" />
355 <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" /> 371 <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" />
356 <!-- Shared protein-protein interactions and pathways --> 372 <!-- Shared protein-protein interactions and pathways -->
357 <conditional name="shared_genes"> 373 <conditional name="shared_genes">
358 <param name="shared_genes_select" type="select" label="Add annotations for shared interactions/pathways?"> 374 <param name="shared_genes_select" type="select" label="Add annotations for shared interactions/pathways?">
359 <option value="yes">Yes</option> 375 <option value="yes">Yes</option>
360 <option value="no" selected="true">No</option> 376 <option value="no" selected="true">No</option>
361 </param> 377 </param>