Merge pull request #5689 from bernt-matthias/bump/mitos2

Bump MITOS and MITOS2
galaxyproject · Jan 19, 2024 · 2d87b0b · 2d87b0b
2 parents ab36a3c + 7758d22
commit 2d87b0b
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Showing 4 changed files with 15 additions and 196 deletions.
diff --git 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
 

diff --git 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@">1.1.4</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>
@@ -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/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@">2.1.6</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/test-data/NC_012920_trnA.svg b/tools/mitos/test-data/NC_012920_trnA.svg