From d8dea5f5ab32c3d83d58d062ce97692b35a9265d Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 21 Dec 2023 10:07:25 +0100
Subject: [PATCH 1/6] bump MITOS2

---
 tools/mitos/mitos2.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/mitos/mitos2.xml b/tools/mitos/mitos2.xml
index dd795ad8811..d32666baf04 100644
--- a/tools/mitos/mitos2.xml
+++ b/tools/mitos/mitos2.xml
@@ -1,14 +1,14 @@
 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>de-novo annotation of metazoan mitochondrial genomes</description>
-  <xrefs>
-      <xref type='bio.tools'>mitos</xref>
-  </xrefs>
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS2</token>
-    <token name="@TOOL_VERSION@">2.1.3</token>
+    <token name="@TOOL_VERSION@">2.1.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
+  <xrefs>
+      <xref type='bio.tools'>mitos</xref>
+  </xrefs>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
   </requirements>

From 5d7433ed817273cb70c525ff1efbea07b18c4a76 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 21 Dec 2023 10:25:45 +0100
Subject: [PATCH 2/6] Use double quotes

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 tools/mitos/mitos2.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mitos/mitos2.xml b/tools/mitos/mitos2.xml
index d32666baf04..13b6677258a 100644
--- a/tools/mitos/mitos2.xml
+++ b/tools/mitos/mitos2.xml
@@ -7,7 +7,7 @@
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <xrefs>
-      <xref type='bio.tools'>mitos</xref>
+      <xref type="bio.tools">mitos</xref>
   </xrefs>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>

From 32a3d8a917d7068574a388b5a9eed32e247b3f04 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 21 Dec 2023 10:27:19 +0100
Subject: [PATCH 3/6] Fix help rst

---
 tools/mitos/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mitos/macros.xml b/tools/mitos/macros.xml
index 876c26d82c8..dd661ca89cd 100644
--- a/tools/mitos/macros.xml
+++ b/tools/mitos/macros.xml
@@ -7,7 +7,7 @@
 
 - A fasta formatted sequence
 
-  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection". The resulting collection can then used as input to @MITOS_NAME@.
+  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection*. The resulting collection can then used as input to @MITOS_NAME@.
   
 - The correct genetic code needs to be selected
 

From 04cc2c15438b5d73418f2b80e0e3c426182f0253 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 23 Dec 2023 09:43:06 +0100
Subject: [PATCH 4/6] bump mitos1 and 2

---
 tools/mitos/mitos.xml  | 8 ++++----
 tools/mitos/mitos2.xml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/mitos/mitos.xml b/tools/mitos/mitos.xml
index 498636e279f..99dd46de09e 100644
--- a/tools/mitos/mitos.xml
+++ b/tools/mitos/mitos.xml
@@ -1,14 +1,14 @@
 <tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>de-novo annotation of metazoan mitochondrial genomes</description>
-  <xrefs>
-      <xref type='bio.tools'>mitos</xref>
-  </xrefs>
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS</token>
-    <token name="@TOOL_VERSION@">1.1.1</token>
+    <token name="@TOOL_VERSION@">1.1.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
+  <xrefs>
+      <xref type='bio.tools'>mitos</xref>
+  </xrefs>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
   </requirements>
diff --git a/tools/mitos/mitos2.xml b/tools/mitos/mitos2.xml
index 13b6677258a..22e43a86be2 100644
--- a/tools/mitos/mitos2.xml
+++ b/tools/mitos/mitos2.xml
@@ -3,7 +3,7 @@
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS2</token>
-    <token name="@TOOL_VERSION@">2.1.4</token>
+    <token name="@TOOL_VERSION@">2.1.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <xrefs>

From 4e3af02aeac079d21c9f142f8b683c73a9989133 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 9 Jan 2024 18:46:47 +0100
Subject: [PATCH 5/6] bump

---
 tools/mitos/mitos.xml  | 2 +-
 tools/mitos/mitos2.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/mitos/mitos.xml b/tools/mitos/mitos.xml
index 99dd46de09e..dca85c0e209 100644
--- a/tools/mitos/mitos.xml
+++ b/tools/mitos/mitos.xml
@@ -3,7 +3,7 @@
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS</token>
-    <token name="@TOOL_VERSION@">1.1.3</token>
+    <token name="@TOOL_VERSION@">1.1.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <xrefs>
diff --git a/tools/mitos/mitos2.xml b/tools/mitos/mitos2.xml
index 22e43a86be2..0dd291b20d0 100644
--- a/tools/mitos/mitos2.xml
+++ b/tools/mitos/mitos2.xml
@@ -3,7 +3,7 @@
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS2</token>
-    <token name="@TOOL_VERSION@">2.1.5</token>
+    <token name="@TOOL_VERSION@">2.1.6</token>
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <xrefs>

From 7758d22d47906b4ab09cad4884ade30514b50b0b Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 10 Jan 2024 16:01:55 +0100
Subject: [PATCH 6/6] fix test

---
 tools/mitos/mitos.xml                    |   7 +-
 tools/mitos/test-data/NC_012920_trnA.svg | 186 -----------------------
 2 files changed, 6 insertions(+), 187 deletions(-)
 delete mode 100644 tools/mitos/test-data/NC_012920_trnA.svg

diff --git a/tools/mitos/mitos.xml b/tools/mitos/mitos.xml
index dca85c0e209..e73e8a0cfb4 100644
--- a/tools/mitos/mitos.xml
+++ b/tools/mitos/mitos.xml
@@ -166,7 +166,12 @@ runmitos.py
       <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
       <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
       <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="24">
-         <element name="trnA-5586-5654" file="NC_012920_trnA.svg" ftype="svg" /> 
+         <element name="trnA-5586-5654" ftype="svg">
+          <assert_contents>
+            <has_text text="&lt;svg"/>
+            <has_size min="100"/>
+          </assert_contents>
+         </element>
       </output_collection>
       <assert_command>
         <has_text text="--code 2"/>
diff --git a/tools/mitos/test-data/NC_012920_trnA.svg b/tools/mitos/test-data/NC_012920_trnA.svg
deleted file mode 100644
index d40e49062e5..00000000000
--- a/tools/mitos/test-data/NC_012920_trnA.svg
+++ /dev/null
@@ -1,186 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<svg xmlns="http://www.w3.org/2000/svg" height="452" width="452">
-<script type="text/ecmascript">
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