From f8452c78ae837b0e006034d00d1c818ade9b56d3 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 24 Nov 2022 13:25:58 +0100
Subject: [PATCH] use more generic setup

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 .../converters/interval_to_bgzip_converter.xml         | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index c809212abe5..9d3e9ba6f52 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -6,10 +6,12 @@
     </requirements>
     <command><![CDATA[
         python '$__tool_directory__/bgzip.py'
-        #if $input1.ext in ['bed', 'gff', 'vcf']
-            -P $input1.ext
-        #elif $input1.ext in ['gtf', 'gff3']
-            -P 'gff'
+        #if $input1.is_of_type('bed')
+            -P bed
+        #elif $input1.is_of_type('vcf')
+            -P vcf
+        #elif $input1.is_of_type('gff')
+            -P gff
         #else
             -c ${input1.metadata.chromCol}
             -s ${input1.metadata.startCol}