From fa60c4863a5ee73a1d73f9cd7e71748ea7d6ff91 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Wed, 17 Jul 2024 12:37:42 +0200
Subject: [PATCH 1/4] Added -a parameter for organism selection

---
 tools/mitohifi/mitohifi.xml | 75 +++++++++++++++++++++++++++++++------
 1 file changed, 64 insertions(+), 11 deletions(-)

diff --git a/tools/mitohifi/mitohifi.xml b/tools/mitohifi/mitohifi.xml
index 48b05e0833..ba4795d220 100644
--- a/tools/mitohifi/mitohifi.xml
+++ b/tools/mitohifi/mitohifi.xml
@@ -30,6 +30,7 @@
             #end if
             -f related_mito.fasta
             -g related_mito.gb
+            -a $operation_mode.organism_selection
             #if $operation_mode.advanced_options.query_blast
                 -p $operation_mode.advanced_options.query_blast
             #end if
@@ -99,6 +100,11 @@
                 <param name="reference_genbank" argument="-g" type="data"
                     format="genbank,genbank.gz" multiple="True" optional="True" label="Close-related mitogenome in genbank format"
                     help="Close-related mitogenome is genbank format"/>
+                <param name="organism_selection" argument="-a" type="select" label="Choose between animal or plant">
+                    <option value="animal" selected="true">Animal</option>
+                    <option value="plant">Plant</option>
+                    <option value="fungal">Fungal</option>
+                </param> 
                 <param name="genetic_code" type="select" label="Genetic code" help="Organism genetic code following NCBI table (for mitogenome annotation)">
                         <option value="1">Standard code</option>
                         <option value="2">Vertebrate mitochondrial code</option>
@@ -305,7 +311,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!--Test 04-->
+        <!--Test 04--> 
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -350,8 +356,55 @@
                     <has_line line=">ptg000001c"/>
                 </assert_contents>
             </output>
+        </test> 
+        <!--Test 05 Testing -a functionality -->
+        <test expect_num_outputs="8">
+            <conditional name="operation_mode">
+                <param name="command" value="mitohifi"/>
+                <conditional name="input_option">
+                    <param name="input" value="pacbio"/>
+                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
+                </conditional>
+                <param name="reference_fasta" value="related_mitogenome.fasta"/>
+                <param name="reference_genbank" value="related_mitogenome.gb"/>
+                <param name="organism_selection" value="plant"/>
+                <param name="genetic_code" value="5"/>
+                <section name="advanced_options">
+                    <param name="circular_size" value="120000"/>
+                </section>
+            </conditional>
+            <output name="mitogenome_fasta" ftype="fasta">
+                <assert_contents>
+                    <has_size value="15337"/>
+                    <has_line line=">ptg000001c_rotated"/>
+                </assert_contents>
+            </output>
+            <output name="mitogenome_genbank" ftype="genbank">
+                <assert_contents>
+                    <has_size value="30637"/>
+                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                </assert_contents>
+            </output>
+            <output name="hifiasm" ftype="fasta">
+                <assert_contents>
+                    <has_size value="4123737"/>
+                    <has_line line=">m64094_200908_163909/67999/ccs"/>
+                </assert_contents>
+            </output>
+            <output name="hifiasm_filtered" ftype="fasta">
+                <assert_contents>
+                    <has_size value="4191948"/>
+                    <has_line line=">m64094_200908_163909/1605/ccs"/>
+                </assert_contents>
+            </output>
+            <output name="hifiasm_contigs" ftype="fasta">
+                <assert_contents>
+                    <has_size value="15329"/>
+                    <has_line line=">ptg000001c"/>
+                </assert_contents>
+            </output>
         </test>
-        <!--Test 05-->
+        <!--Test 06 -->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -396,8 +449,8 @@
                     <has_line line=">ptg000001c"/>
                 </assert_contents>
             </output>
-        </test>
-        <!--Test 06-->
+        </test> 
+        <!--Test 07 -->
         <test expect_num_outputs="11">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -459,7 +512,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!--Test 07-->
+        <!--Test 08 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -509,8 +562,8 @@
                     <has_size value="28"/>
                 </assert_contents>
             </output>
-        </test>
-        <!--Test 08-->
+        </test> 
+        <!--Test 09 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -561,8 +614,8 @@
                     <has_line line=">ptg000001c"/>
                 </assert_contents>
             </output>
-        </test>
-        <!--Test 09-->
+        </test> 
+        <!--Test 10 -->
         <test expect_num_outputs="2">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -586,8 +639,8 @@
                     <has_line line="DEFINITION  NC_016067.1_rc_rotated"/>
                 </assert_contents>
             </output>
-        </test>
-        <!--Test 10-->
+        </test> 
+        <!--Test 11 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>

From 6fa948903fe8e9ba9cc3c70fa358b46f582b2281 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Wed, 17 Jul 2024 12:37:51 +0200
Subject: [PATCH 2/4] updated macros.xml

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

diff --git a/tools/mitohifi/macros.xml b/tools/mitohifi/macros.xml
index a6902af06c..9e3e1aa3a6 100644
--- a/tools/mitohifi/macros.xml
+++ b/tools/mitohifi/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy1</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0196</edam_topic>

From 73aa4909139901d2f3941749a34b1082fd4559d1 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Thu, 18 Jul 2024 11:12:56 +0200
Subject: [PATCH 3/4] Updated test cases

---
 tools/mitohifi/mitohifi.xml | 177 ++++++++++++++++++------------------
 1 file changed, 89 insertions(+), 88 deletions(-)

diff --git a/tools/mitohifi/mitohifi.xml b/tools/mitohifi/mitohifi.xml
index ba4795d220..aefb97304e 100644
--- a/tools/mitohifi/mitohifi.xml
+++ b/tools/mitohifi/mitohifi.xml
@@ -211,14 +211,14 @@
             </conditional>
             <output name="fasta_reference" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15593"/>
-                    <has_line line=">NC_062101.1 Condica capensis mitochondrion, complete genome"/>
+                    <has_size value="15662"/>
+                    <has_line line=">PP230663.1 Spodoptera frugiperda isolate HC93 mitochondrion, complete genome"/>
                 </assert_contents>
             </output>
             <output name="genbank_reference" ftype="genbank">
                 <assert_contents>
-                    <has_size value="43220"/>
-                    <has_line line="DEFINITION  Condica capensis mitochondrion, complete genome."/>
+                    <has_size value="36693"/>
+                    <has_line line="DEFINITION  Spodoptera frugiperda isolate HC93 mitochondrion, complete genome."/>
                 </assert_contents>
             </output>
         </test>
@@ -265,7 +265,7 @@
                 </assert_contents>
             </output>
         </test>-->
-        <!--Test 03-->
+         <!--Test 02-->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -282,36 +282,36 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
         </test>
-        <!--Test 04--> 
+        <!--Test 03--> 
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -328,36 +328,36 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="30768"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="53052"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
         </test> 
-        <!--Test 05 Testing -a functionality -->
+        <!--Test 04 (Testing -a flag)--> 
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -375,36 +375,36 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="30768"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="53052"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
-        </test>
-        <!--Test 06 -->
+        </test> 
+        <!--Test 05 -->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -421,36 +421,37 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
         </test> 
-        <!--Test 07 -->
+
+        <!--Test 06 -->
         <test expect_num_outputs="11">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -467,52 +468,52 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <!--<has_line line=">m64094_200908_163909/1605/ccs"/>-->
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="parsed_blast" ftype="txt">
                 <assert_contents>
-                    <has_size value="104"/>
+                    <has_size value="105"/>
                  </assert_contents>
             </output>
             <output name="parsed_blast_all" ftype="txt">
                 <assert_contents>
-                    <has_size value="104"/>
+                    <has_size value="105"/>
                 </assert_contents>
             </output>
             <output name="contigs_ids" ftype="txt">
                 <assert_contents>
                     <has_size value="11"/>
-                    <has_line line="ptg000001c"/>
+                    <has_line line="ptg000001l"/>
                 </assert_contents>
             </output>
         </test>
-        <!--Test 08 -->
+        <!--Test 07 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -529,41 +530,41 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="contigs_circularization" ftype="txt">
                 <assert_contents>
-                    <has_size value="28"/>
+                    <has_size value="55"/>
                 </assert_contents>
             </output>
-        </test> 
-        <!--Test 09 -->
+        </test>
+        <!--Test 08 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -580,42 +581,42 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="final_mitogenome" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="55"/>
+                    <!-- <has_line line=">ptg000001c"/> -->
                 </assert_contents>
             </output>
         </test> 
-        <!--Test 10 -->
+        <!--Test 09 -->
         <test expect_num_outputs="2">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -639,8 +640,8 @@
                     <has_line line="DEFINITION  NC_016067.1_rc_rotated"/>
                 </assert_contents>
             </output>
-        </test> 
-        <!--Test 11 -->
+        </test>
+        <!--Test 10 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -655,40 +656,40 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="30637"/>
-                    <has_line line="DEFINITION  ptg000001c_rotated"/>
+                    <has_size value="30548"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4123737"/>
+                    <has_size value="3963527"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4191948"/>
+                    <has_size value="4029085"/>
                     <has_line line=">m64094_200908_163909/1605/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_contigs" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
             <output name="zip_file" ftype="zip">
                 <assert_contents>
-                    <has_size value="5418006" delta="100"/>
+                    <has_size value="5190456" delta="100"/>
                 </assert_contents>
             </output>
-        </test>
+        </test>     
     </tests>
     <help><![CDATA[
 .. class:: infomark

From 8fa6dc60cd8d28f47866e405b1c019953301815b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 19 Jul 2024 14:16:23 +0200
Subject: [PATCH 4/4] use the new image

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

diff --git a/tools/mitohifi/macros.xml b/tools/mitohifi/macros.xml
index 9e3e1aa3a6..8fcebee330 100644
--- a/tools/mitohifi/macros.xml
+++ b/tools/mitohifi/macros.xml
@@ -11,7 +11,7 @@
     </xml>
     <xml name="requirements">
         <requirements>
-            <container type="docker">quay.io/bgruening/mitohifi:3_galaxy0</container>
+            <container type="docker">quay.io/bgruening/mitohifi:@TOOL_VERSION@_@GALAXY_TOOL_VERSION@</container>
         </requirements>
     </xml>
     <xml name="citations">