From a058dd0b7a0921d5fb97781203deb6c8860ea0af Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 8 Sep 2023 11:57:50 +0200
Subject: [PATCH 1/9] bump converters using samtools

and use tmpdir consistently

for me most important to get https://github.com/samtools/samtools/releases/tag/1.14
because of

> Improved samtools sort use of temporary files, both tidying up if it fails and recovery when facing pre-existing temporary files.

The old versions apparently do not delete files in /tmp for failed
jobs which causes problems on my site (due to my resubmission
strategy I have more failing jobs than other sites I guess).
---
 lib/galaxy/datatypes/converters/bam_to_bai.xml              | 4 ++--
 lib/galaxy/datatypes/converters/cram_to_bam_converter.xml   | 4 ++--
 lib/galaxy/datatypes/converters/fasta_to_fai.xml            | 4 ++--
 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml | 4 ++--
 lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml     | 4 ++--
 .../datatypes/converters/to_coordinate_sorted_bam.xml       | 6 +++---
 lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml     | 6 +++---
 7 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
index e33a0a7bb9b4..c18472fc627f 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bai.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -1,6 +1,6 @@
-<tool id="CONVERTER_Bam_Bai_0" name="Convert Bam to Bai" version="1.0.0" hidden="true" profile="16.04">
+<tool id="CONVERTER_Bam_Bai_0" name="Convert Bam to Bai" version="1.0.1" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package" version="1.10">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </requirements>
     <command>samtools index -@ \${GALAXY_SLOTS:-1} '$input1' '$output1'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml b/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
index 62bc6e3b845b..b55f48a989cf 100644
--- a/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
+++ b/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
@@ -1,6 +1,6 @@
-<tool id="CONVERTER_cram_to_bam_0" name="Convert CRAM to BAM" version="1.0.1" hidden="true" profile="16.04">
+<tool id="CONVERTER_cram_to_bam_0" name="Convert CRAM to BAM" version="1.0.2" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package" version="1.16.1">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </requirements>
     <command><![CDATA[
         samtools sort -@\${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' --output-fmt BAM '$input'
diff --git a/lib/galaxy/datatypes/converters/fasta_to_fai.xml b/lib/galaxy/datatypes/converters/fasta_to_fai.xml
index 747438acc3b3..da2581847ac0 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_fai.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_fai.xml
@@ -1,6 +1,6 @@
-<tool id="CONVERTER_fasta_to_fai" name="Convert FASTA to fai file" version="1.0.0">
+<tool id="CONVERTER_fasta_to_fai" name="Convert FASTA to fai file" version="1.0.1">
     <requirements>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </requirements>
     <command><![CDATA[
 ln -s '$input' temp.fasta &&
diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
index 905949c45a9e..6dc0111f6bff 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
-<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.3" hidden="true">
     <requirements>
         <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
         <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
diff --git a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
index b8982dd0f165..8a708f601076 100644
--- a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
@@ -1,6 +1,6 @@
-<tool id="CONVERTER_sam_to_unsorted_bam" name="Convert SAM to BAM without sorting" version="1.0.0" profile="18.01">
+<tool id="CONVERTER_sam_to_unsorted_bam" name="Convert SAM to BAM without sorting" version="1.0.1" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </requirements>
     <command><![CDATA[
         samtools view
diff --git a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
index ce3933523e32..19e758ff94e1 100644
--- a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
@@ -1,13 +1,13 @@
-<tool id="CONVERTER_bam_to_coodinate_sorted_bam" name="Convert BAM to coordinate-sorted BAM" version="1.0.0" hidden="true" profile="18.01">
+<tool id="CONVERTER_bam_to_coodinate_sorted_bam" name="Convert BAM to coordinate-sorted BAM" version="1.0.1" hidden="true" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </requirements>
     <command><![CDATA[
          samtools sort
             -@ \${GALAXY_SLOTS:-1}
             -o '${output}'
             -O bam
-            -T dataset
+            -T "\${TMPDIR:-.}"
             '${input}'
     ]]>
     </command>
diff --git a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
index 8cdb77e3e9ad..f10e95aca98d 100644
--- a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
@@ -1,6 +1,6 @@
-<tool id="CONVERTER_bam_to_qname_sorted_bam" name="Convert BAM to queryname-sorted BAM" version="1.0.0" hidden="true" profile="18.01">
+<tool id="CONVERTER_bam_to_qname_sorted_bam" name="Convert BAM to queryname-sorted BAM" version="1.0.1" hidden="true" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </requirements>
     <command><![CDATA[
          samtools sort
@@ -8,7 +8,7 @@
             -o '${output}'
             -n
             -O bam
-            -T dataset
+            -T "\${TMPDIR:-.}" 
             '${input}'
     ]]>
     </command>

From 2117385d135355671c27eecf891489d54e05ab9f Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 8 Sep 2023 13:16:52 +0200
Subject: [PATCH 2/9] fix framework test

by allowing lines_diff
---
 test/functional/tools/sam_to_bam.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/functional/tools/sam_to_bam.xml b/test/functional/tools/sam_to_bam.xml
index 3420ed73ec9a..15299f8be3ef 100644
--- a/test/functional/tools/sam_to_bam.xml
+++ b/test/functional/tools/sam_to_bam.xml
@@ -11,7 +11,8 @@ cat '$input1' > '$out_file1'
     <tests>
         <test>
             <param name="input1" value="sam_with_header.sam" ftype="sam"/>
-            <output name="out_file1" file="bam_from_sam.bam" ftype="bam"/>
+            <!-- allow up to 2 differences (4 lines) due to version change of the implicitly running converter  -->
+            <output name="out_file1" file="bam_from_sam.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>
     <help>

From 71a105f72df46c65c4237cb4f351387bf7f436c0 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 8 Sep 2023 14:05:06 +0200
Subject: [PATCH 3/9] add converters to workflow safe updates

---
 lib/galaxy/tools/__init__.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index e7c52a1af0f8..6af20f6eb695 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -298,6 +298,12 @@ class safe_update(NamedTuple):
     "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
     "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "CONVERTER_fasta_to_fai": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_sam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
+    "CONVERTER_bam_to_coodinate_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_bam_to_qname_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
 }
 
 

From 434e8840a973fe5bbf35b6d9b92942b8babee478 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 8 Sep 2023 14:21:13 +0200
Subject: [PATCH 4/9] update all requirements

---
 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
index 6dc0111f6bff..a7bf7c975fe0 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
 <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.3" hidden="true">
     <requirements>
-        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
         <requirement type="package" version="1.18">samtools</requirement>
-        <requirement type="package" version="2.27.1">bedtools</requirement>
+        <requirement type="package" version="2.31.0">bedtools</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 samtools view -bh '$input' | bedtools genomecov -bg -split -ibam stdin

From a1771fb0ca326ecd3eec8fcfed041c597427d931 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 8 Sep 2023 18:26:27 +0200
Subject: [PATCH 5/9] try to fix tests

---
 lib/galaxy/datatypes/converters/bam_to_bai.xml               | 2 +-
 lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml      | 1 +
 lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml | 4 +++-
 lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml      | 4 +++-
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
index c18472fc627f..8810bd03c47a 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bai.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -2,7 +2,7 @@
     <requirements>
         <requirement type="package" version="1.18">samtools</requirement>
     </requirements>
-    <command>samtools index -@ \${GALAXY_SLOTS:-1} '$input1' '$output1'</command>
+    <command>samtools index -@ \${GALAXY_SLOTS:-1} -b '$input1' -o '$output1'</command>
     <inputs>
         <param format="bam" name="input1" type="data" label="Choose BAM"/>
     </inputs>
diff --git a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
index 8a708f601076..77c4f2450335 100644
--- a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
@@ -7,6 +7,7 @@
             -b
             -h
             -@ \${GALAXY_SLOTS:-2}
+            --no-PG
             -o '${output}'
             '$input'
     ]]>
diff --git a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
index 19e758ff94e1..d6075d2d77cb 100644
--- a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
@@ -5,6 +5,7 @@
     <command><![CDATA[
          samtools sort
             -@ \${GALAXY_SLOTS:-1}
+            --no-PG
             -o '${output}'
             -O bam
             -T "\${TMPDIR:-.}"
@@ -20,7 +21,8 @@
     <tests>
         <test>
             <param name="input" ftype="sam" value="bfast_out1.sam"/>
-            <output name="output" ftype="bam" value="bfast_out1.bam"/>
+            <!--lines diff due to @HD line which contained GO:none before-->
+            <output name="output" ftype="bam" value="bfast_out1.bam" lines_diff="2"/>
         </test>
     </tests>
     <help>
diff --git a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
index f10e95aca98d..e75eb2c6446b 100644
--- a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
@@ -7,6 +7,7 @@
             -@ \${GALAXY_SLOTS:-1}
             -o '${output}'
             -n
+            --no-PG
             -O bam
             -T "\${TMPDIR:-.}" 
             '${input}'
@@ -21,7 +22,8 @@
     <tests>
         <test>
             <param name="input" ftype="sam" value="bfast_out1.sam"/>
-            <output name="output" ftype="qname_sorted.bam" value="bfast_out1.qname_sorted.bam"/>
+            <!--lines diff due to @HD line which contained GO:none before-->
+            <output name="output" ftype="qname_sorted.bam" value="bfast_out1.qname_sorted.bam" lines_diff="2"/>
         </test>
     </tests>
     <help>

From 0f387f7996e2d81e402a8405abade5235f94fe4b Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 9 Sep 2023 10:42:41 +0200
Subject: [PATCH 6/9] use 1.17 and fix tests

latest available on bioconda
---
 lib/galaxy/datatypes/converters/bam_to_bai.xml            | 8 ++++++--
 lib/galaxy/datatypes/converters/cram_to_bam_converter.xml | 2 +-
 lib/galaxy/datatypes/converters/fasta_to_fai.xml          | 2 +-
 .../datatypes/converters/sam_to_bigwig_converter.xml      | 2 +-
 lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml   | 2 +-
 .../datatypes/converters/to_coordinate_sorted_bam.xml     | 2 +-
 lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml   | 2 +-
 7 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
index 8810bd03c47a..9a3726fe5c1a 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bai.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_Bam_Bai_0" name="Convert Bam to Bai" version="1.0.1" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package" version="1.18">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command>samtools index -@ \${GALAXY_SLOTS:-1} -b '$input1' -o '$output1'</command>
     <inputs>
@@ -12,7 +12,11 @@
     <tests>
         <test>
             <param name="input1" ftype="bam" value="srma_out2.bam"/>
-            <output name="output1" ftype="bai" value="srma_out2.bai"/>
+            <output name="output1" ftype="bai">
+                <assert_contents>
+                    <has_size value="7584" delta="10"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>
diff --git a/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml b/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
index b55f48a989cf..339500a208b7 100644
--- a/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
+++ b/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_cram_to_bam_0" name="Convert CRAM to BAM" version="1.0.2" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package" version="1.18">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
         samtools sort -@\${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' --output-fmt BAM '$input'
diff --git a/lib/galaxy/datatypes/converters/fasta_to_fai.xml b/lib/galaxy/datatypes/converters/fasta_to_fai.xml
index da2581847ac0..9d812f828259 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_fai.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_fai.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_fasta_to_fai" name="Convert FASTA to fai file" version="1.0.1">
     <requirements>
-        <requirement type="package" version="1.18">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
 ln -s '$input' temp.fasta &&
diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
index a7bf7c975fe0..dbdcf9677fc5 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.3" hidden="true">
     <requirements>
         <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="1.18">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
         <requirement type="package" version="2.31.0">bedtools</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
diff --git a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
index 77c4f2450335..e67931cdce2a 100644
--- a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_sam_to_unsorted_bam" name="Convert SAM to BAM without sorting" version="1.0.1" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.18">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
         samtools view
diff --git a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
index d6075d2d77cb..7bbc00592f1d 100644
--- a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_bam_to_coodinate_sorted_bam" name="Convert BAM to coordinate-sorted BAM" version="1.0.1" hidden="true" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.18">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
          samtools sort
diff --git a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
index e75eb2c6446b..e1cc013971e5 100644
--- a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_bam_to_qname_sorted_bam" name="Convert BAM to queryname-sorted BAM" version="1.0.1" hidden="true" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.18">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
          samtools sort

From 884140840636f0992e2fac2137c5e6495c9d454a Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 9 Sep 2023 13:19:47 +0200
Subject: [PATCH 7/9] fix functional test

---
 test/functional/tools/sam_to_unsorted_bam.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/functional/tools/sam_to_unsorted_bam.xml b/test/functional/tools/sam_to_unsorted_bam.xml
index 3a0830e8838a..cb7f710ea5b6 100644
--- a/test/functional/tools/sam_to_unsorted_bam.xml
+++ b/test/functional/tools/sam_to_unsorted_bam.xml
@@ -56,17 +56,17 @@
         <!-- Test that sam input is properly converted to bam -->
         <test>
             <param name="input3" value="sam_with_header.sam" ftype="sam"/>
-            <output name="bam_output" file="bam_from_sam.bam" ftype="bam"/>
+            <output name="bam_output" file="bam_from_sam.bam" ftype="bam" lines_diff="2"/>
         </test>
         <!-- Test that sam input is properly converted to qname_sorted.bam -->
         <test>
             <param name="input4" value="sam_with_header.sam" ftype="sam"/>
-            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam"/>
+            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam" lines_diff="2"/>
         </test>
         <!-- Test that sam input is properly converted to qname_sorted.bam (which is qname_input_sorted.bam compatible) -->
         <test>
             <param name="input4" value="sam_with_header.sam" ftype="sam"/>
-            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam"/>
+            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam" lines_diff="2"/>
         </test>
     </tests>
     <help>

From 8912293cc4783f32546faa9769fa8d5785858550 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 9 Sep 2023 14:31:48 +0200
Subject: [PATCH 8/9] update other converters using ucsc* and bedtools

---
 .../datatypes/converters/bam_to_bigwig_converter.xml      | 8 ++++----
 .../converters/bed_gff_or_vcf_to_bigwig_converter.xml     | 6 +++---
 .../datatypes/converters/bedgraph_to_bigwig_converter.xml | 4 ++--
 .../datatypes/converters/bigwig_to_wig_converter.xml      | 2 +-
 .../datatypes/converters/interval_to_bgzip_converter.xml  | 6 +++---
 .../datatypes/converters/interval_to_bigwig_converter.xml | 8 ++++----
 .../datatypes/converters/wig_to_bigwig_converter.xml      | 2 +-
 lib/galaxy/tools/__init__.py                              | 8 +++++++-
 8 files changed, 25 insertions(+), 19 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index 7c321587b994..ec08741e1d55 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,9 +1,9 @@
-<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.3" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.29.2">bedtools</requirement>
-        <requirement type="package" version="8.25">coreutils</requirement>
+        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.31.0">bedtools</requirement>
+        <requirement type="package" version="9.4">coreutils</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 bedtools genomecov -bg -split -ibam '$input'
diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
index 47dd1f4b158a..184595a3acbd 100644
--- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
-<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.1" hidden="true">
+<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.2" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.27.1">bedtools</requirement>
+        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.31.0">bedtools</requirement>
     </requirements>
     <command>
 <![CDATA[
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
index d102c838c36f..a9f6204725c7 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
-<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.1" hidden="true">
+<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.2" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
-        <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
+        <requirement type="package" version="445">ucsc-wigtobigwig</requirement>
     </requirements>
     <command>grep -v "^track" '$input' | wigToBigWig -clip stdin '$chromInfo' '$output'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml b/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
index 08a37b045716..05d07e2a4128 100644
--- a/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="bigwigtowig" name="Convert BigWig to Wiggle" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
     <description>Convert bigWig to wig</description>
     <macros>
-        <token name="@TOOL_VERSION@">377</token>
+        <token name="@TOOL_VERSION@">445</token>
         <token name="@SUFFIX_VERSION@">0</token>
     </macros>
     <requirements>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 52e1e8d7b98f..4580a958494d 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="1.0.3" hidden="true" profile="16.04">
+<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.4" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <macros>
         <xml name="assert_size" tokens="value" token_delta="10">
@@ -9,8 +9,8 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="9.1">coreutils</requirement>
-        <requirement type="package" version="1.16">htslib</requirement>
+        <requirement type="package" version="9.4">coreutils</requirement>
+        <requirement type="package" version="1.17">htslib</requirement>
     </requirements>
     <command><![CDATA[
         ## Skip any lines starting with '#' and 'track'
diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
index b394a655431d..bae538b38fe0 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -1,9 +1,9 @@
-<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.1">
+<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.2">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.29.2">bedtools</requirement>
-        <requirement type="package" version="8.25">coreutils</requirement>
+        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.31.0">bedtools</requirement>
+        <requirement type="package" version="9.4">coreutils</requirement>
     </requirements>
     <command>
 <![CDATA[
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index 62d418f78a48..7b95504e91ab 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.1" hidden="true">
+<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.2" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
         <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 6af20f6eb695..6ffd7eb9ecef 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -297,13 +297,19 @@ class safe_update(NamedTuple):
     "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
     "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
-    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "bigwigtowig": safe_update(parse_version("377+galaxy0"), parse_version("445+galaxy0")),
+    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.4")),
     "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_bed_gff_or_vcf_to_bigwig_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "CONVERTER_bedgraph_to_bigwig": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_fasta_to_fai": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_interval_to_bigwig_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_sam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
+    "CONVERTER_bam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
     "CONVERTER_bam_to_coodinate_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "CONVERTER_bam_to_qname_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_wig_to_bigwig": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
 }
 
 

From b2a3208424585b05188d58b45bac10d43defd743 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 9 Sep 2023 17:02:48 +0200
Subject: [PATCH 9/9] Revert "update other converters using ucsc* and bedtools"

This reverts commit 8912293cc4783f32546faa9769fa8d5785858550.
---
 .../datatypes/converters/bam_to_bigwig_converter.xml      | 8 ++++----
 .../converters/bed_gff_or_vcf_to_bigwig_converter.xml     | 6 +++---
 .../datatypes/converters/bedgraph_to_bigwig_converter.xml | 4 ++--
 .../datatypes/converters/bigwig_to_wig_converter.xml      | 2 +-
 .../datatypes/converters/interval_to_bgzip_converter.xml  | 6 +++---
 .../datatypes/converters/interval_to_bigwig_converter.xml | 8 ++++----
 .../datatypes/converters/wig_to_bigwig_converter.xml      | 2 +-
 lib/galaxy/tools/__init__.py                              | 8 +-------
 8 files changed, 19 insertions(+), 25 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index ec08741e1d55..7c321587b994 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,9 +1,9 @@
-<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.3" hidden="true">
+<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.2" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.31.0">bedtools</requirement>
-        <requirement type="package" version="9.4">coreutils</requirement>
+        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.29.2">bedtools</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 bedtools genomecov -bg -split -ibam '$input'
diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
index 184595a3acbd..47dd1f4b158a 100644
--- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
-<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.1" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.31.0">bedtools</requirement>
+        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command>
 <![CDATA[
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
index a9f6204725c7..d102c838c36f 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
-<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.1" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
-        <requirement type="package" version="445">ucsc-wigtobigwig</requirement>
+        <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
     </requirements>
     <command>grep -v "^track" '$input' | wigToBigWig -clip stdin '$chromInfo' '$output'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml b/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
index 05d07e2a4128..08a37b045716 100644
--- a/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="bigwigtowig" name="Convert BigWig to Wiggle" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
     <description>Convert bigWig to wig</description>
     <macros>
-        <token name="@TOOL_VERSION@">445</token>
+        <token name="@TOOL_VERSION@">377</token>
         <token name="@SUFFIX_VERSION@">0</token>
     </macros>
     <requirements>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 4580a958494d..52e1e8d7b98f 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="1.0.4" hidden="true" profile="16.04">
+<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.3" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <macros>
         <xml name="assert_size" tokens="value" token_delta="10">
@@ -9,8 +9,8 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="9.4">coreutils</requirement>
-        <requirement type="package" version="1.17">htslib</requirement>
+        <requirement type="package" version="9.1">coreutils</requirement>
+        <requirement type="package" version="1.16">htslib</requirement>
     </requirements>
     <command><![CDATA[
         ## Skip any lines starting with '#' and 'track'
diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
index bae538b38fe0..b394a655431d 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -1,9 +1,9 @@
-<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.2">
+<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.1">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.31.0">bedtools</requirement>
-        <requirement type="package" version="9.4">coreutils</requirement>
+        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.29.2">bedtools</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
     </requirements>
     <command>
 <![CDATA[
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index 7b95504e91ab..62d418f78a48 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.1" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
         <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 6ffd7eb9ecef..6af20f6eb695 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -297,19 +297,13 @@ class safe_update(NamedTuple):
     "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
     "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
-    "bigwigtowig": safe_update(parse_version("377+galaxy0"), parse_version("445+galaxy0")),
-    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.4")),
+    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_bed_gff_or_vcf_to_bigwig_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
-    "CONVERTER_bedgraph_to_bigwig": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_fasta_to_fai": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_interval_to_bigwig_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_sam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
-    "CONVERTER_bam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
     "CONVERTER_bam_to_coodinate_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "CONVERTER_bam_to_qname_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_wig_to_bigwig": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
 }