# HG changeset patch
# User iuc
# Date 1656412875 0
# Node ID 27fd1c1f00a8de4d9e3a710eda9800f112bbeca5
# Parent  7303183cdb87e0798a0d26c8f6e0a07c3b83dd89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 1d05f91b90a92d0c6c60a635711704fe93e00562

diff -r 7303183cdb87 -r 27fd1c1f00a8 ensembl_vep.xml
--- a/ensembl_vep.xml	Wed May 11 13:03:38 2022 +0000
+++ b/ensembl_vep.xml	Tue Jun 28 10:41:15 2022 +0000
@@ -1,7 +1,8 @@
-<tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@">
+<tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
 	<description>with VEP</description>
 	<macros>
 		<token name="@TOOL_VERSION@">106.1</token>
+		<token name="@VERSION_SUFFIX@">1</token>
 		<token name="@DB_VERSION@">106</token>
 		<xml name="vcf_input">
 			<param type="data" name="input1" label="VCF input file" format="vcf">
@@ -27,6 +28,12 @@
 			bgzip -c > 'custom_annotation.${custom_ext}.gz' &&
 			tabix -p gff 'custom_annotation.${custom_ext}.gz' &&
 		#end if
+		#if $ref_seq.ref_source == "cached":
+			ln -s '$ref_seq.ref.fields.path' reference.fa &&
+		#else if $ref_seq.ref_source == "history":
+			ln -s '$ref_seq.ref' reference.fa &&
+		#end if
+		
 		vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf
 		#if $annotation_cache.source == "custom":
 			--$custom_ext 'custom_annotation.${custom_ext}.gz'
@@ -40,10 +47,8 @@
 			## The --offline flag automatically activates --cache. This is not wanted in our gff/gtf case but also not needed as no internet connection is required for annotating with these custom annotation sources.
 			--offline
 		#end if
-		#if $ref_seq.ref_source == "cached":
-			--fasta '${ref_seq.ref.fields.path}'
-		#elif $ref_seq.ref_source == "history":
-			--fasta '${ref_seq.ref}'
+		#if $ref_seq.ref_source != "no_ref"
+			--fasta reference.fa
 		#end if
 		--stats_text