--- a/mitos2.xml	Wed Mar 01 22:38:41 2023 +0000
+++ b/mitos2.xml	Wed Dec 10 23:30:17 2025 +0000
@@ -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@">2.1.10</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>
@@ -16,7 +16,7 @@
   <command detect_errors="aggressive"><![CDATA[
 mkdir outdir &&
 
-runmitos.py
+runmitos
 --input '$input'
 --code $code
 --outdir outdir
@@ -47,7 +47,7 @@
 --maxtrnaovl $advanced_ncrna.maxtrnaovl
 --maxrrnaovl $advanced_ncrna.maxrrnaovl
 
-#if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
+#if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs or "ncRNA_structure_svg_plots" in $addoutputs):
   --noplots
 #end if
 #if "raw" in str($addoutputs).split(','):
@@ -64,11 +64,15 @@
     </param> 
     <param argument="--code" label="Genetic code" type="select">
       <option value="2">Vertebrate (2)</option>
+      <option value="3">Yeast (3)</option>
       <option value="4">Mold, Protozoan, Coelenteral (4)</option>
       <option value="5">Invertebrate (5)</option>
       <option value="9">Echinoderm, Flatworm (9)</option>
       <option value="13">Ascidian (13)</option>
       <option value="14">Alternative Flatworm (14)</option>
+      <option value="21">Trematode (21)</option>
+      <option value="24">Rhabdopleuridae (24)</option>
+      <option value="33">Cephalodiscidae (33)</option>
     </param>
     <param argument="--refseqver" label="Reference data" type="select" help="Contact the administrator of this Galaxy instance if you miss reference data">
         <options from_data_table="mitos">
@@ -294,17 +298,18 @@
       </assert_command>
     </test>
     <!-- missing genes -->
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <param name="input" value="NC_012920.fasta"/>
       <param name="code" value="2"/>
       <param name="refseqver" value="mitos2-refdata" />
-      <param name="addoutputs" value="bed,missing"/>
+      <param name="addoutputs" value="bed,missing,ncRNA_structure_svg_plots"/>
       <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
       <output name="missing_genes" ftype="txt">
         <assert_contents>
           <has_size value="167"/>
         </assert_contents>
       </output>
+      <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="5"/>
       <assert_command>
         <has_text text="--code 2"/>
         <has_text text="--finovl 50"/>
@@ -323,7 +328,7 @@
         <has_text text="--ncev 0.01"/>
         <has_text text="--maxtrnaovl 50"/>
         <has_text text="--maxrrnaovl 50"/>
-        <has_text text="--noplots"/>
+        <has_text text="--noplots" negate="true"/>
       </assert_command>
     </test>
   </tests>