From 1168d9b6b5299337744e1172b22302f78cd6d639 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 14 Dec 2023 12:17:01 +0100
Subject: [PATCH 1/3] unintrusive fix for converter tests

---
 .../interval_to_bgzip_converter.xml           | 37 ++++++++++++++-----
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 52e1e8d7b98f..6bc11fb5888d 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -40,9 +40,12 @@
     <tests>
         <test>
             <param name="input1" ftype="bed" value="droPer1.bed"/>
-            <output name="output1" ftype="bgzip" value="droPer1.bgzip" decompress="true">
+            <output name="output1" ftype="bgzip" value="droPer1.bgzip">
                 <expand macro="assert_size" value="131"/>
             </output>
+            <output name="output1" ftype="bgzip" decompress="true">
+                <expand macro="assert_size" value="120"/>
+            </output>
             <assert_command>
                 <has_text text="-k1,1 -k2,2n -k3,3n"/>
             </assert_command>
@@ -50,6 +53,9 @@
         <test>
             <param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
             <output name="output1" ftype="bgzip">
+                <expand macro="assert_size" value="141"/>
+            </output>
+            <output name="output1" ftype="bgzip" decompress="true">
                 <expand macro="assert_size" value="143">
                     <has_text_matching expression="^#" negate="true"/>
                 </expand>
@@ -60,9 +66,12 @@
         </test>
         <test>
             <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>
-            <output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
+            <output name="output1" ftype="bgzip">
                 <expand macro="assert_size" value="638"/>
             </output>
+            <output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
+                <expand macro="assert_size" value="3824"/>
+            </output>
             <assert_command>
                 <has_text text="-k1,1 -k4,4n"/>
                 <has_text text="-k5,5" negate="true"/>
@@ -70,20 +79,25 @@
         </test>
         <test>
             <param name="input1" ftype="interval" value="2.interval"/>
-            <output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
+            <output name="output1" ftype="bgzip">
                 <expand macro="assert_size" value="208"/>
             </output>
+            <output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
+                <expand macro="assert_size" value="501"/>
+            </output>
             <assert_command>
                 <has_text text="-k1,1 -k2,2n -k3,3n"/>
             </assert_command>
         </test>
         <test>
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
+            <output name="output1" ftype="bgzip">
+                <expand macro="assert_size" value="321"/>
+            </output>
             <output name="output1" ftype="bgzip" decompress="true">
-                <expand macro="assert_size" value="322">
-                    <!-- will only work with https://github.com/galaxyproject/galaxy/pull/15085
-                        <has_n_lines n="3"/>
-                        <has_text_matching expression="^#" negate="true"/> -->
+                <expand macro="assert_size" value="507">
+                    <has_n_lines n="5"/>
+                    <has_text_matching expression="^#" negate="true"/>
                 </expand>
             </output>
             <assert_command>
@@ -92,9 +106,14 @@
         </test>
         <test>
             <param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
-            <output name="output1" ftype="bgzip" >
+            <output name="output1" ftype="bgzip">
+                <assert_contents>
+                    <has_size value="270" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="output1" ftype="bgzip" decompress="true">
                 <assert_contents>
-                    <has_size value="270" delta="10" />
+                    <has_size value="887"/>
                 </assert_contents>
             </output>
             <assert_command>

From ef225c490feb8d235607680264ab93e64b247732 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 14 Dec 2023 12:20:55 +0100
Subject: [PATCH 2/3] slighly more intrusive fix

---
 .../interval_to_bgzip_converter.xml           | 22 +------------------
 1 file changed, 1 insertion(+), 21 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 6bc11fb5888d..fe1df3514d19 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -40,10 +40,7 @@
     <tests>
         <test>
             <param name="input1" ftype="bed" value="droPer1.bed"/>
-            <output name="output1" ftype="bgzip" value="droPer1.bgzip">
-                <expand macro="assert_size" value="131"/>
-            </output>
-            <output name="output1" ftype="bgzip" decompress="true">
+            <output name="output1" ftype="bgzip" value="droPer1.bgzip" decompress="true">
                 <expand macro="assert_size" value="120"/>
             </output>
             <assert_command>
@@ -52,9 +49,6 @@
         </test>
         <test>
             <param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="141"/>
-            </output>
             <output name="output1" ftype="bgzip" decompress="true">
                 <expand macro="assert_size" value="143">
                     <has_text_matching expression="^#" negate="true"/>
@@ -66,9 +60,6 @@
         </test>
         <test>
             <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="638"/>
-            </output>
             <output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
                 <expand macro="assert_size" value="3824"/>
             </output>
@@ -79,9 +70,6 @@
         </test>
         <test>
             <param name="input1" ftype="interval" value="2.interval"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="208"/>
-            </output>
             <output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
                 <expand macro="assert_size" value="501"/>
             </output>
@@ -91,9 +79,6 @@
         </test>
         <test>
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
-            <output name="output1" ftype="bgzip">
-                <expand macro="assert_size" value="321"/>
-            </output>
             <output name="output1" ftype="bgzip" decompress="true">
                 <expand macro="assert_size" value="507">
                     <has_n_lines n="5"/>
@@ -106,11 +91,6 @@
         </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>
             <output name="output1" ftype="bgzip" decompress="true">
                 <assert_contents>
                     <has_size value="887"/>

From b4ae0a4a4bf6c5647c22d29c5006147096d70609 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 14 Dec 2023 14:50:11 +0100
Subject: [PATCH 3/3] Also fix test of the vcf_to_vcf_bgzip_converter

---
 lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
index 41617707e2b9..f6ebadcf1d34 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
@@ -17,7 +17,7 @@
             <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
             <output name="output1" ftype="vcf_bgzip" value="vcf_bgzip_to_maf_in.vcf_bgzip" decompress="true">
                 <assert_contents>
-                    <has_size value="717" delta="10"/>
+                    <has_size value="1182"/>
                 </assert_contents>
             </output>
         </test>