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 1/4] 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>

From 737b112ad757d4dc3b5270d4e3fd5dfc12355b78 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 23 Nov 2022 16:56:07 +0100
Subject: [PATCH 2/4] bump version

---
 lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml | 2 +-
 lib/galaxy/tools/__init__.py                                    | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index d3ee80dab07..c809212abe5 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.1" hidden="true" profile="16.04">
+<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.2" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
         <requirement type="package" version="0.15.4">pysam</requirement>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c4b7c2ef25a..d717040f3f0 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -281,6 +281,7 @@ WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
     "Show beginning1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.2")),
     "Show tail1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
     "sort1": safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.2.0")),
+    "CONVERTER_interval_to_bgzip_0": safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.2"))
 }
 
 

From d98cbfa5512f12db7433478451f58537d5ec3798 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 23 Nov 2022 17:01:23 +0100
Subject: [PATCH 3/4] run black

---
 lib/galaxy/tools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index d717040f3f0..9baa9f12278 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -281,7 +281,7 @@ WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
     "Show beginning1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.2")),
     "Show tail1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
     "sort1": safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.2.0")),
-    "CONVERTER_interval_to_bgzip_0": safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.2"))
+    "CONVERTER_interval_to_bgzip_0": safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.2")),
 }
 
 

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 4/4] 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}