# HG changeset patch
# User bgruening
# Date 1683142389 0
# Node ID 99ddbf037d98fcaccfd8a62d0a686ba34def5327
# Parent  f6065bc6e42874dbdd6d6d9d2efb427e0216f01b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit 59301409d1f555702e346d7b6ba3992a4f336691

diff -r f6065bc6e428 -r 99ddbf037d98 macros.xml
--- a/macros.xml	Sat May 29 12:50:32 2021 +0000
+++ b/macros.xml	Wed May 03 19:33:09 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2</token>
+    <token name="@TOOL_VERSION@">3</token>
     <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
@@ -11,12 +11,12 @@
     </xml>
     <xml name="requirements">
         <requirements>
-            <container type="docker">quay.io/bgruening/mitohifi:2_galaxy0</container>
+            <container type="docker">quay.io/bgruening/mitohifi:3_galaxy0</container>
         </requirements>
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1111/1755-0998.13160</citation>
+            <citation type="doi">10.1101/2022.12.23.521667</citation>
         </citations>
     </xml>
 </macros>
diff -r f6065bc6e428 -r 99ddbf037d98 mitohifi.xml
--- a/mitohifi.xml	Sat May 29 12:50:32 2021 +0000
+++ b/mitohifi.xml	Wed May 03 19:33:09 2023 +0000
@@ -14,14 +14,14 @@
             #if $operation_mode.min_length
                 --min_length $operation_mode.min_length
             #end if
-            $operation_mode.exact_specie
+            $operation_mode.exact_species
             && mv ./*fasta ./reference_genome.fasta
             && mv ./*gb ./reference_genome.gb
         #elif $operation_mode.command == 'mitohifi'
             ln -s '${operation_mode.reference_genbank}' related_mito.gb
             && ln -s '${operation_mode.reference_fasta}' related_mito.fasta
 
-            && mitohifi_v2.py 
+            && mitohifi.py 
             #if $operation_mode.input_option.input == 'pacbio'
                 -r '${ ' '.join(["%s" % $x for $x in $operation_mode.input_option.input_reads]) }'
                 -m $operation_mode.input_option.bloom_filter
@@ -53,7 +53,7 @@
                 <option value="mitohifi">Run MitoHiFi</option>
             </param>
             <when value="find_reference">
-                <param argument="--species" type="text" value="" label="Specie name" help="Specie name in binomial nomenclature">
+                <param argument="--species" type="text" value="" label="Species name" help="Species name in binomial nomenclature">
                     <sanitizer invalid_char="">
                         <valid initial="string.letters,string.digits">
                             <add value=" "/>
@@ -72,7 +72,7 @@
                 </param>
                 <param argument="--min_length" type="integer" 
                     min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" />
-                <param name="exact_specie" argument="-s" type="boolean" 
+                <param name="exact_species" argument="-s" type="boolean" 
                     truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/>
             </when>
             <when value="mitohifi">
@@ -153,6 +153,15 @@
         <data name="mitogenome_genbank" format="genbank" from_work_dir="final_mitogenome.gb" label="${tool.name} on ${on_string}: final mitogenome (genbank)">
             <filter> operation_mode['command'] == 'mitohifi'</filter>
         </data>
+        <data name="mitogenome_annotation" format="png" from_work_dir="final_mitogenome.annotation.png" label="${tool.name} on ${on_string}: final mitogenome annotation (png)">
+            <filter> operation_mode['command'] == 'mitohifi'</filter>
+        </data>
+        <data name="mitogenome_coverage" format="png" from_work_dir="final_mitogenome.coverage.png" label="${tool.name} on ${on_string}: final mitogenome coverage (png)">
+            <filter> operation_mode['command'] == 'mitohifi'</filter>
+        </data>
+        <data name="contigs_stats" format="tsv" from_work_dir="contigs_stats.tsv" label="${tool.name} on ${on_string}: contigs stats (TSV)">
+            <filter> operation_mode['command'] == 'mitohifi'</filter>
+        </data>
         <data name="parsed_blast" format="txt" from_work_dir="contigs_filtering/parsed_blast.txt" label="${tool.name} on ${on_string}: parsed BLAST">
             <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>
         </data> 
@@ -196,19 +205,19 @@
             </conditional>
             <output name="fasta_reference" ftype="fasta">
                 <assert_contents>
-                    <has_size value="15742"/>
-                    <has_line line=">NC_054179.1 Spodoptera exempta mitochondrion, complete genome"/>
+                    <has_size value="15593"/>
+                    <has_line line=">NC_062101.1 Condica capensis mitochondrion, complete genome"/>
                 </assert_contents>
             </output>
             <output name="genbank_reference" ftype="genbank">
                 <assert_contents>
-                    <has_size value="43468"/>
-                    <has_line line="DEFINITION  Spodoptera exempta mitochondrion, complete genome."/>
+                    <has_size value="43220"/>
+                    <has_line line="DEFINITION  Condica capensis mitochondrion, complete genome."/>
                 </assert_contents>
             </output>
         </test>
         <!--Test 02-->
-        <test expect_num_outputs="5">
+        <!--<test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -249,9 +258,9 @@
                     <has_line line=">ptg000001c"/>
                 </assert_contents>
             </output>
-        </test>
+        </test>-->
         <!--Test 03-->
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -297,7 +306,7 @@
             </output>
         </test>
         <!--Test 04-->
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -343,7 +352,7 @@
             </output>
         </test>
         <!--Test 05-->
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="8">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -389,7 +398,7 @@
             </output>
         </test>
         <!--Test 06-->
-        <test expect_num_outputs="8">
+        <test expect_num_outputs="11">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -451,7 +460,7 @@
             </output>
         </test>
         <!--Test 07-->
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -502,7 +511,7 @@
             </output>
         </test>
         <!--Test 08-->
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">
@@ -579,7 +588,7 @@
             </output>
         </test>
         <!--Test 10-->
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="9">
             <conditional name="operation_mode">
                 <param name="command" value="mitohifi"/>
                 <conditional name="input_option">