# HG changeset patch
# User elixir-it
# Date 1540457164 14400
# Node ID bfd92976550f8299f584fbb8f4214e004758b216
# Parent  7a54ac4976d0300f6a032574623f6f0289fab393
Uploaded

diff -r 7a54ac4976d0 -r bfd92976550f .shed.yml
--- /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
diff -r 7a54ac4976d0 -r bfd92976550f vep_unico.xml
--- 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
 		 ]]>