diff --git a/tools/mitohifi/macros.xml b/tools/mitohifi/macros.xml
index a6902af06c..8fcebee330 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>
@@ -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">
diff --git a/tools/mitohifi/mitohifi.xml b/tools/mitohifi/mitohifi.xml
index 48b05e0833..aefb97304e 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>
@@ -205,14 +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>
@@ -259,7 +265,7 @@
                 </assert_contents>
             </output>
         </test>-->
-        <!--Test 03-->
+         <!--Test 02-->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -276,36 +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"/>
@@ -322,36 +328,83 @@
             </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-->
+        </test> 
+        <!--Test 04 (Testing -a flag)--> 
+        <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="30768"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
+                </assert_contents>
+            </output>
+            <output name="mitogenome_genbank" ftype="genbank">
+                <assert_contents>
+                    <has_size value="53052"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
+                </assert_contents>
+            </output>
+            <output name="hifiasm" ftype="fasta">
+                <assert_contents>
+                    <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="4029085"/>
+                    <has_line line=">m64094_200908_163909/1605/ccs"/>
+                </assert_contents>
+            </output>
+            <output name="hifiasm_contigs" ftype="fasta">
+                <assert_contents>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
+                </assert_contents>
+            </output>
+        </test> 
+        <!--Test 05 -->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -368,36 +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 06-->
+        </test> 
+
+        <!--Test 06 -->
         <test expect_num_outputs="11">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -414,52 +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 07-->
+        <!--Test 07 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -476,41 +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 08-->
+        <!--Test 08 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -527,42 +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 09-->
+        </test> 
+        <!--Test 09 -->
         <test expect_num_outputs="2">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -587,7 +641,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!--Test 10-->
+        <!--Test 10 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -602,40 +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