Mercurial > repos > elixir-it > vep86_vcf2maf

changeset 2:bfd92976550f draft

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Uploaded
author elixir-it
date Thu, 25 Oct 2018 04:46:04 -0400
parents 7a54ac4976d0
children ca1e48c52db9
files .shed.yml vep_unico.xml
diffstat 2 files changed, 13 insertions(+), 2 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Thu Oct 25 04:46:04 2018 -0400
@@ -0,0 +1,10 @@
+categories:
+- Variant Analysis
+description: 'vep86_vcf2maf: vep86 determines the effect of your variants vcf2maf same thing but giving the output in MAF format '
+homepage_url: https://www.ensembl.org/info/docs/tools/vep/index.html https://github.com/mskcc/vcf2maf
+long_description: |
+VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.vcf2mafuse VEP and give the output in MAF format 
+name: vep86_vcf2maf
+owner: elixir-it
+remote_repository_url: https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/vep86_vcf2maf-wrapper
+type: unrestricted
--- a/vep_unico.xml	Mon Oct 01 11:21:05 2018 -0400
+++ b/vep_unico.xml	Thu Oct 25 04:46:04 2018 -0400
@@ -29,7 +29,7 @@
 	
 	#if str($veptools.veptoolsselect) =="annotate"
 	 perl \$CONDA_DEFAULT_ENV/bin/variant_effect_predictor.pl
-        --fork \${GALAXY_SLOTS:-4}
+        --fork 4
         --offline
         --dir \$CONDA_DEFAULT_ENV/vep_cache
         --force_overwrite
@@ -57,7 +57,8 @@
             --vep-path \$CONDA_DEFAULT_ENV/bin/
             --vep-data \$CONDA_DEFAULT_ENV/vep_cache
             --ref-fasta $veptools.reference
-            --species $veptools.species;
+            --species $veptools.species
+	    --filter-vcf 0 ;
 
         #end if
 		 ]]>