diff kggseq_variant_selection.xml @ 4:a13b8ff61c6c draft

planemo upload

--- a/kggseq_variant_selection.xml	Mon May 25 18:01:25 2015 -0400
+++ b/kggseq_variant_selection.xml	Thu Aug 04 04:40:06 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.3">
+<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.4">
   <description></description>
   <requirements>
-    <requirement type="package" version="0.8_20150423 ">kggseq</requirement>
+    <requirement type="package" version="1.0_0_20160412">kggseq</requirement>
   </requirements>
   <command>
 java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
@@ -13,6 +13,7 @@
 --no-progress-check
 --out results
 --o-vcf
+--no-gz
 
 --vcf-file $inputFile
 --ped-file $pedFile
@@ -126,9 +127,16 @@
   #end if
   $add_annotations.genome_annotation
   $add_annotations.omim_annotation
-  $add_annotations.cosmic_annotation
+  $add_annotations.cosmic_annotation  
+  $add_annotations.scsnv_annotation
+  $add_annotations.dgv_cnv_annotation
+  $add_annotations.superdup_annotation
+  $add_annotations.mouse_pheno_annotation
+  $add_annotations.zebrafish_pheno_annotation
+  $add_annotations.ddd_annotation
+  $add_annotations.patho_gene_predict_annotation  
   #if $add_annotations.pubmed_mining_gene
-    $add_annotations.pubmed_type "$add_annotations.pubmed_mining_gene"
+    --phenotype-term "$add_annotations.pubmed_mining_gene" --pubmed-mining
   #end if
   #if str($add_annotations.shared_genes.shared_genes_select) == "yes"
     --ppi-annot string
@@ -277,7 +285,12 @@
         <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)">
+        <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)">			
+		  <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>
+		  <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>
+		  <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>
+		  <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>
+		  <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>			
           <option value="1kg201305" selected="true">1KG 201305: 1000 Genomes Project 2013 May release</option>
           <option value="1kg201204">1KG 201204: 1000 Genomes Project 2012 April release</option>
           <option value="1kgafr201204">1KG 201204 AFR: 1000 Genomes Project 2012 April release - African</option>
@@ -347,13 +360,16 @@
         <param name="o_flanking_seq" type="integer" value="" optional="true" label="Size in bp of flanking sequence to extract (--o-flanking-seq)" />
         <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="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" />		
+		<param name="scsnv_annotation" type="boolean" truevalue="--scsnv-annot" falsevalue="" checked="true" label="Potential of altering splicing (--scsnv-annot)" />
+		<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)" />
+		<param name="superdup_annotation" type="boolean" truevalue="--superdup-annot" falsevalue="" checked="true" label="Mark the variants in the super duplicate regions (--superdup-annot)" />
+		<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)" />
+		<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)" />
+		<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)" />
+		<param name="patho_gene_predict_annotation" type="boolean" truevalue="--patho-gene-predict" falsevalue="" checked="true" label="Predict genes’ pathogenicity (--patho-gene-predict)" />
         <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 -->
+		<!-- 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>