From 34ee04287d8e6bb356fb129f53259b5799d85a8b Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 23 Nov 2022 14:16:00 +0100
Subject: [PATCH] fix interval_to_bgzip for sub gff classes

---
 .../converters/interval_to_bgzip_converter.xml         | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 9eab8ea4c53..d3ee80dab07 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -8,6 +8,8 @@
         python '$__tool_directory__/bgzip.py'
         #if $input1.ext in ['bed', 'gff', 'vcf']
             -P $input1.ext
+        #elif $input1.ext in ['gtf', 'gff3']
+            -P 'gff'
         #else
             -c ${input1.metadata.chromCol}
             -s ${input1.metadata.startCol}
@@ -47,6 +49,14 @@
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
             <output name="output1" ftype="bgzip" value="bgzip_to_maf_in.bgzip"/>
         </test>
+        <test>
+            <param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
+            <output name="output1" ftype="bgzip" >
+                <assert_contents>
+                    <has_size value="270" delta="10" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
     </help>