# HG changeset patch
# User bgruening
# Date 1746538586 0
# Node ID bfab6f5b449d28d2c6f95479e35439ef97169c42
# Parent  99ddbf037d98fcaccfd8a62d0a686ba34def5327
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit 3faa0723d5faf734d8821626bbd31a614b25aafb

diff -r 99ddbf037d98 -r bfab6f5b449d macros.xml
--- a/macros.xml	Wed May 03 19:33:09 2023 +0000
+++ b/macros.xml	Tue May 06 13:36:26 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
+    <token name="@TOOL_VERSION@">3.2.3</token>
+    <token name="@VERSION_SUFFIX@">0</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">ghcr.io/marcelauliano/mitohifi:@TOOL_VERSION@</container>
         </requirements>
     </xml>
     <xml name="citations">
diff -r 99ddbf037d98 -r bfab6f5b449d mitohifi.xml
--- a/mitohifi.xml	Wed May 03 19:33:09 2023 +0000
+++ b/mitohifi.xml	Tue May 06 13:36:26 2025 +0000
@@ -1,10 +1,10 @@
-<tool id='mitohifi' name='MitoHiFi' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
-    <description>assembly mitogenomes from Pacbio HiFi reads</description>
+<tool id='mitohifi' name='MitoHiFi' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='23.2'>
+    <description>Assemble mitogenomes from Pacbio HiFi reads</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro='edam_ontology' />
-    <expand macro='requirements' />
+    <expand macro='edam_ontology'/>
+    <expand macro='requirements'/>
     <command detect_errors='exit_code'><![CDATA[
         #if $operation_mode.command == 'find_reference'
             findMitoReference.py 
@@ -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
@@ -71,7 +72,7 @@
                     </sanitizer>
                 </param>
                 <param argument="--min_length" type="integer" 
-                    min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" />
+                    min="0" max="15000000" value="" optional="True" label="Minimal appropriate length"/>
                 <param name="exact_species" argument="-s" type="boolean" 
                     truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/>
             </when>
@@ -94,11 +95,16 @@
                     </when>
                 </conditional>
                 <param name="reference_fasta" argument="-f" type="data"
-                    format="fasta,fasta.gz" multiple="True" label="Close-related mitogenome in fasta format"
+                    format="fasta,fasta.gz" label="Close-related mitogenome in fasta format"
                     help="Close-related mitogenome is fasta format"/>
                 <param name="reference_genbank" argument="-g" type="data"
-                    format="genbank,genbank.gz" multiple="True" optional="True" label="Close-related mitogenome in genbank format"
+                    format="genbank,genbank.gz" 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>
@@ -122,13 +128,13 @@
                 <section name="advanced_options" title="Advanced options">
                     <param name="query_blast" argument="-p" type="integer" 
                         min="0" max="100" value="" optional="True" label="Blast percentage identity"
-                        help="Percentage of query in the blast match with close-related mito. By default it is going to chose any contig which has 50% or more of its length in the blast match." />
+                        help="Percentage of query in the blast match with close-related mito. By default it is going to chose any contig which has 50% or more of its length in the blast match."/>
                     <param argument="--circular-size" type="integer" 
                         min="0" max="15000000" value="" optional="True" label="Estimated mtDNA size"
-                        help="Size to consider when checking for circularization" />
+                        help="Size to consider when checking for circularization"/>
                     <param argument="--circular_offset" type="integer" 
                         min="0" max="5000" value="" optional="True" label="Circularization offset" 
-                        help="Offset from start and finish to consider when looking for circularization" />
+                        help="Offset from start and finish to consider when looking for circularization"/>
                     <param name="outputs" type="select" label="Optional outputs" multiple="True" display="checkboxes">
                         <option value="contigs_filtering">Contigs filtering</option>
                         <option value="contigs_circularization">Contigs circularization</option>
@@ -136,7 +142,7 @@
                         <option value="final_mitogenome_alignment">Final mitogenome alignment</option>
                     </param>
                 </section>
-                <param name="output_zip" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate an output package in ZIP format" help="This option creates a zip file with all the files and folders generated by MitoHiFi." />
+                <param name="output_zip" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate an output package in ZIP format" help="This option creates a zip file with all the files and folders generated by MitoHiFi."/>
             </when>
         </conditional>
     </inputs>
@@ -175,7 +181,7 @@
             <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_circularization' in operation_mode['advanced_options']['outputs'])</filter>
         </data>
         <collection name="potential_contigs" type='list' label='${tool.name} on ${on_string}: potential contigs'>
-            <discover_datasets pattern='__designation_and_ext__' format='txt' directory='potential_contigs' />
+            <discover_datasets pattern='__designation_and_ext__' format='txt' directory='potential_contigs'/>
             <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'potential_contigs' in operation_mode['advanced_options']['outputs'])</filter>
         </collection>
         <data name="final_mitogenome" format="fasta" from_work_dir="final_mitogenome_choice/all_mitogenomes.rotated.aligned.fa" label="${tool.name} on ${on_string}: mitogenomes alignment">
@@ -205,19 +211,19 @@
             </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" delta="200"/>
+                    <has_line line=">OQ539671.1 Amphipyra erebina 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="35605" delta="200"/>
+                    <has_line line="DEFINITION  Amphipyra erebina mitochondrion, complete genome."/>
                 </assert_contents>
             </output>
         </test>
         <!--Test 02-->
-        <!--<test expect_num_outputs="8">
+        <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -230,36 +236,36 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="15603" delta="200"/>
+                    <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" delta="200"/>
+                    <has_line line="DEFINITION  ptg000001l."/>
                 </assert_contents>
             </output>
             <output name="hifiasm" ftype="fasta">
                 <assert_contents>
-                    <has_size value="2063025"/>
+                    <has_size value="1956147"/>
                     <has_line line=">m64094_200908_163909/67999/ccs"/>
                 </assert_contents>
             </output>
             <output name="hifiasm_filtered" ftype="fasta">
                 <assert_contents>
-                    <has_size value="2097153"/>
+                    <has_size value="1988506"/>
                     <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 03-->
+        </test>
+         <!--Test 03-->
         <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 04--> 
         <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="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 05 --> 
+        <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="15603"/>
+                    <has_line line=">ptg000001l_rotated ptg000001l"/>
                 </assert_contents>
             </output>
-        </test>
-        <!--Test 05-->
+            <output name="mitogenome_genbank" ftype="genbank">
+                <assert_contents>
+                    <has_size value="30548"/>
+                    <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 06 -->
         <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -368,36 +421,36 @@
             </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 06-->
+        </test> 
+        <!--Test 07 -->
         <test expect_num_outputs="11">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -414,52 +467,51 @@
             </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_line line=">m64094_200908_163909/1605/ccs"/>-->
+                    <has_size value="4029085"/>
                 </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 08 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -476,94 +528,42 @@
             </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"/>
-                </assert_contents>
-            </output>
-            <output name="contigs_circularization" ftype="txt">
-                <assert_contents>
-                    <has_size value="28"/>
-                </assert_contents>
-            </output>
-        </test>
-        <!--Test 08-->
-        <test expect_num_outputs="9">
-            <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="genetic_code" value="5"/>
-                <section name="advanced_options">
-                    <param name="outputs" value="contigs_circularization"/>
-                </section>
-            </conditional>
-            <output name="mitogenome_fasta" ftype="fasta">
-                <assert_contents>
-                    <has_size value="15337"/>
-                    <has_line line=">ptg000001c_rotated"/>
+                    <has_size value="30246"/>
+                    <has_line line=">ptg000001l"/>
                 </assert_contents>
             </output>
-            <output name="mitogenome_genbank" ftype="genbank">
+            <output name="contigs_circularization">
                 <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"/>
+                    <has_size value="55"/>
                 </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>
-            <output name="final_mitogenome" ftype="fasta">
-                <assert_contents>
-                    <has_size value="15329"/>
-                    <has_line line=">ptg000001c"/>
-                </assert_contents>
-            </output>
-        </test>
-        <!--Test 09-->
-        <test expect_num_outputs="2">
+        </test> 
+        <!--Test 09 -->
+        <test expect_num_outputs="5">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -576,18 +576,33 @@
             </conditional>
             <output name="mitogenome_fasta" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15684"/>
+                    <has_size value="15944"/>
                     <has_line line=">NC_016067.1_rc_rotated"/>
                 </assert_contents>
             </output>
             <output name="mitogenome_genbank" ftype="genbank">
                 <assert_contents>
-                    <has_size value="31407"/>
-                    <has_line line="DEFINITION  NC_016067.1_rc_rotated"/>
+                    <has_size value="31411"/>
+                    <has_line line="ACCESSION   NC_016067.1_rc_rotated"/>
+                </assert_contents>
+            </output>
+            <output name="mitogenome_genbank" ftype="genbank">
+                <assert_contents>
+                    <has_line line="ACCESSION   NC_016067.1_rc_rotated"/>
+                </assert_contents>
+            </output>
+            <output name="mitogenome_annotation" ftype="png">
+                <assert_contents>
+                    <has_size value="67255"/>
+                </assert_contents>
+            </output>
+            <output name="contigs_stats" ftype="tsv">
+                <assert_contents>
+                    <has_n_lines n="4"/>
                 </assert_contents>
             </output>
         </test>
-        <!--Test 10-->
+        <!--Test 10 -->
         <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
@@ -602,40 +617,40 @@
             </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
@@ -653,5 +668,5 @@
 
 
     ]]>    </help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>