# HG changeset patch
# User iuc
# Date 1765409417 0
# Node ID 6cd432abcf8e6f7eeff89ba66e5a686072554a81
# Parent  c8f5229645ef8ff31b139aaa274f1084cb9af9bb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos commit 24a59e271fbe0b87d826d1d36b3a9ea008227adc

diff -r c8f5229645ef -r 6cd432abcf8e macros.xml
--- a/macros.xml	Wed Mar 01 22:38:41 2023 +0000
+++ b/macros.xml	Wed Dec 10 23:30:17 2025 +0000
@@ -7,7 +7,7 @@
 
 - A fasta formatted sequence
 
-  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection". The resulting collection can then used as input to @MITOS_NAME@.
+  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection*. The resulting collection can then used as input to @MITOS_NAME@.
   
 - The correct genetic code needs to be selected
 
diff -r c8f5229645ef -r 6cd432abcf8e mitos2.xml
--- 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>
diff -r c8f5229645ef -r 6cd432abcf8e test-data/NC_012920.gff
--- a/test-data/NC_012920.gff	Wed Mar 01 22:38:41 2023 +0000
+++ b/test-data/NC_012920.gff	Wed Dec 10 23:30:17 2025 +0000
@@ -1,25 +1,28 @@
-NC_012920	mitfi	tRNA	577	647	1.127e-05	+	.	Name=trnF(gaa)	; model Y; evalue 0.000011; pvalue 0.000000; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	1602	1670	1.671e-06	+	.	Name=trnV(tac)	; model A; evalue 0.000002; pvalue 0.000000; qstart 1; qstop 65
-NC_012920	mitfi	tRNA	3230	3304	0.0006685	+	.	Name=trnL2(taa)	; model Y; evalue 0.000669; pvalue 0.000001; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	4263	4331	5.584e-05	+	.	Name=trnI(gat)	; model Y; evalue 0.000056; pvalue 0.000000; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	4329	4400	0.097	-	.	Name=trnQ(ttg)	; model Y; evalue 0.097000; pvalue 0.000096; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	4402	4469	0.001232	+	.	Name=trnM(cat)	; model A; evalue 0.001232; pvalue 0.000001; qstart 1; qstop 65
-NC_012920	mitfi	tRNA	5512	5579	0.001059	+	.	Name=trnW(tca)	; model Y; evalue 0.001059; pvalue 0.000001; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	5587	5655	1.529e-08	-	.	Name=trnA(tgc)	; model A; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 65
-NC_012920	mitfi	tRNA	5659	5721	0.1419	-	.	Name=trnN(gtt)	; model Y; evalue 0.141900; pvalue 0.000140; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	5761	5826	0.0006482	-	.	Name=trnC(gca)	; model Y; evalue 0.000648; pvalue 0.000001; qstart 1; qstop 68
-NC_012920	mitfi	rRNA	5761	5826	2.104e-11	-	.	Name=rrnS	; model rrnS; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 66
-NC_012920	mitfi	tRNA	5827	5891	1.031e-09	-	.	Name=trnY(gta)	; model Y; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	7446	7514	0.0475	-	.	Name=trnS2(tga)	; model Y; evalue 0.047500; pvalue 0.000047; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	7518	7585	0.0005019	+	.	Name=trnD(gtc)	; model A; evalue 0.000502; pvalue 0.000000; qstart 1; qstop 65
-NC_012920	mitfi	rRNA	7518	7585	7.886e-12	+	.	Name=rrnL	; model rrnL; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 67
-NC_012920	mitfi	tRNA	8295	8364	0.0007967	+	.	Name=trnK(ttt)	; model Y; evalue 0.000797; pvalue 0.000001; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	9991	10058	7.29e-06	+	.	Name=trnG(tcc)	; model A; evalue 0.000007; pvalue 0.000000; qstart 1; qstop 65
-NC_012920	mitfi	tRNA	10405	10469	2.068e-06	+	.	Name=trnR(tcg)	; model A; evalue 0.000002; pvalue 0.000000; qstart 1; qstop 65
-NC_012920	mitfi	tRNA	12138	12206	2.765e-06	+	.	Name=trnH(gtg)	; model Y; evalue 0.000003; pvalue 0.000000; qstart 1; qstop 68
-NC_012920	mitfi	tRNA	12266	12336	0.09648	+	.	Name=trnL1(tag)	; model A; evalue 0.096480; pvalue 0.000093; qstart 1; qstop 65
-NC_012920	mitfi	rRNA	12770	12817	0.1077	-	.	Name=rrnS	; model rrnS; evalue 0.107700; pvalue 0.000099; qstart 1; qstop 66
+##gff-version 3
+#!gff-spec-version 1.21
+NC_012920	mitos	region	1	16569	.	+	.	ID=NC_012920:1..16569;Is_circular=False;Name=NC_012920;genome=mitochondrion;mol_type=genomic DNA
+NC_012920	mitfi	tRNA	577	647	1.127e-05	+	.	Name=trnF(gaa)
+NC_012920	mitfi	tRNA	1602	1670	1.671e-06	+	.	Name=trnV(tac)
+NC_012920	mitfi	tRNA	3230	3304	0.0006685	+	.	Name=trnL2(taa)
+NC_012920	mitfi	tRNA	4263	4331	5.584e-05	+	.	Name=trnI(gat)
+NC_012920	mitfi	tRNA	4329	4400	0.097	-	.	Name=trnQ(ttg)
+NC_012920	mitfi	tRNA	4402	4469	0.001232	+	.	Name=trnM(cat)
+NC_012920	mitfi	tRNA	5512	5579	0.001059	+	.	Name=trnW(tca)
+NC_012920	mitfi	tRNA	5587	5655	1.529e-08	-	.	Name=trnA(tgc)
+NC_012920	mitfi	tRNA	5659	5721	0.1419	-	.	Name=trnN(gtt)
+NC_012920	mitfi	tRNA	5761	5826	0.0006482	-	.	Name=trnC(gca)
+NC_012920	mitfi	rRNA	5761	5826	2.104e-11	-	.	Name=rrnS
+NC_012920	mitfi	tRNA	5827	5891	1.031e-09	-	.	Name=trnY(gta)
+NC_012920	mitfi	tRNA	7446	7514	0.0475	-	.	Name=trnS2(tga)
+NC_012920	mitfi	tRNA	7518	7585	0.0005019	+	.	Name=trnD(gtc)
+NC_012920	mitfi	rRNA	7518	7585	7.886e-12	+	.	Name=rrnL
+NC_012920	mitfi	tRNA	8295	8364	0.0007967	+	.	Name=trnK(ttt)
+NC_012920	mitfi	tRNA	9991	10058	7.29e-06	+	.	Name=trnG(tcc)
+NC_012920	mitfi	tRNA	10405	10469	2.068e-06	+	.	Name=trnR(tcg)
+NC_012920	mitfi	tRNA	12138	12206	2.765e-06	+	.	Name=trnH(gtg)
+NC_012920	mitfi	tRNA	12266	12336	0.09648	+	.	Name=trnL1(tag)
+NC_012920	mitfi	rRNA	12770	12817	0.1077	-	.	Name=rrnS
 NC_012920	mitos	gene	14155	14673	24486974.4	-	.	Name=nad6
-NC_012920	mitfi	tRNA	14674	14742	3.085e-06	-	.	Name=trnE(ttc)	; model A; evalue 0.000003; pvalue 0.000000; qstart 1; qstop 65
-NC_012920	mitfi	tRNA	15888	15953	1.962e-08	+	.	Name=trnT(tgt)	; model A; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 65
-NC_012920	mitfi	tRNA	15956	16023	1.555e-06	-	.	Name=trnP(tgg)	; model A; evalue 0.000002; pvalue 0.000000; qstart 1; qstop 65
+NC_012920	mitfi	tRNA	14674	14742	3.085e-06	-	.	Name=trnE(ttc)
+NC_012920	mitfi	tRNA	15888	15953	1.962e-08	+	.	Name=trnT(tgt)
+NC_012920	mitfi	tRNA	15956	16023	1.555e-06	-	.	Name=trnP(tgg)
diff -r c8f5229645ef -r 6cd432abcf8e test-data/NC_012920.seq
--- a/test-data/NC_012920.seq	Wed Mar 01 22:38:41 2023 +0000
+++ b/test-data/NC_012920.seq	Wed Dec 10 23:30:17 2025 +0000
@@ -39,7 +39,7 @@
 			gene	trnC(gca)
 5826	5761	tRNA
 			product	tRNA-CYS
-5826	5761	gene
+			gene	rrnS
 5826	5761	rRNA
 			product	s-rRNA
 5891	5827	gene
@@ -54,7 +54,7 @@
 			gene	trnD(gtc)
 7518	7585	tRNA
 			product	tRNA-ASP
-7518	7585	gene
+			gene	rrnL
 7518	7585	rRNA
 			product	l-rRNA
 8295	8364	gene
@@ -77,7 +77,7 @@
 			gene	trnL1(tag)
 12266	12336	tRNA
 			product	tRNA-LEU1
-12817	12770	gene
+			gene	rrnS
 12817	12770	rRNA
 			product	s-rRNA
 14673	14155	gene
diff -r c8f5229645ef -r 6cd432abcf8e test-data/NC_012920_trnA.svg
--- a/test-data/NC_012920_trnA.svg	Wed Mar 01 22:38:41 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<svg xmlns="http://www.w3.org/2000/svg" height="452" width="452">
-<script type="text/ecmascript">
-      <![CDATA[
-        var shown = 1;
-        function click() {
-             var seq = document.getElementById("seq");
-             if (shown==1) {
-               seq.setAttribute("style", "visibility: hidden");
-               shown = 0;
-             } else {
-               seq.setAttribute("style", "visibility: visible");
-               shown = 1;
-             }
-         }
-        ]]>
-</script>
-  <rect style="stroke: white; fill: white" height="452" x="0" y="0" width="452" onclick="click(evt)" />
-  <g transform="scale(1.606723,1.606723) translate(25.639824,33.551025)">
-    <polyline style="stroke: black; fill: none; stroke-width: 1.5" id="outline" points="
-      112.164,-10.084
-      111.491,4.901
-      110.818,19.886
-      110.145,34.870
-      109.472,49.855
-      108.799,64.840
-      108.126,79.825
-      92.018,81.598
-      79.209,90.125
-      72.157,102.876
-      57.292,100.862
-      42.428,98.849
-      27.564,96.835
-      16.740,84.993
-      0.744,86.216
-      -8.154,99.565
-      -3.128,114.801
-      11.966,120.235
-      25.550,111.700
-      40.415,113.713
-      55.279,115.727
-      70.143,117.740
-      74.909,130.778
-      85.025,140.285
-      81.034,154.745
-      77.044,169.204
-      73.053,183.663
-      69.063,198.123
-      54.767,204.460
-      47.936,218.527
-      51.795,233.681
-      64.522,242.767
-      80.108,241.495
-      91.193,230.465
-      92.544,214.886
-      83.522,202.113
-      87.513,187.654
-      91.503,173.195
-      95.494,158.735
-      99.484,144.276
-      110.578,143.482
-      120.992,138.597
-      129.225,130.028
-      133.985,118.727
-      134.391,106.090
-      149.376,105.417
-      164.361,104.744
-      179.345,104.071
-      194.330,103.398
-      204.775,115.035
-      220.264,117.185
-      233.484,108.832
-      238.193,93.920
-      232.166,79.490
-      218.251,72.356
-      203.017,75.886
-      193.657,88.413
-      178.673,89.086
-      163.688,89.759
-      148.703,90.432
-      133.718,91.105
-      123.111,80.498
-      123.784,65.513
-      124.457,50.528
-      125.130,35.543
-      125.803,20.559
-      126.476,5.574
-      127.149,-9.411
-      130.202,-28.551
-    " />
-    <g style="stroke: black; stroke-width: 1" id="pairs">
-      <line id="1,68" x1="112.164" y1="-10.084" x2="127.149" y2="-9.411" />
-      <line id="2,67" x1="111.491" y1=" 4.901" x2="126.476" y2=" 5.574" />
-      <line id="3,66" x1="110.818" y1="19.886" x2="125.803" y2="20.559" />
-      <line id="4,65" x1="110.145" y1="34.870" x2="125.130" y2="35.543" />
-      <line id="5,64" x1="109.472" y1="49.855" x2="124.457" y2="50.528" />
-      <line id="6,63" x1="108.799" y1="64.840" x2="123.784" y2="65.513" />
-      <line id="7,62" x1="108.126" y1="79.825" x2="123.111" y2="80.498" />
-      <line id="10,22" x1="72.157" y1="102.876" x2="70.143" y2="117.740" />
-      <line id="11,21" x1="57.292" y1="100.862" x2="55.279" y2="115.727" />
-      <line id="12,20" x1="42.428" y1="98.849" x2="40.415" y2="113.713" />
-      <line id="13,19" x1="27.564" y1="96.835" x2="25.550" y2="111.700" />
-      <line id="24,40" x1="85.025" y1="140.285" x2="99.484" y2="144.276" />
-      <line id="25,39" x1="81.034" y1="154.745" x2="95.494" y2="158.735" />
-      <line id="26,38" x1="77.044" y1="169.204" x2="91.503" y2="173.195" />
-      <line id="27,37" x1="73.053" y1="183.663" x2="87.513" y2="187.654" />
-      <line id="28,36" x1="69.063" y1="198.123" x2="83.522" y2="202.113" />
-      <line id="45,61" x1="134.391" y1="106.090" x2="133.718" y2="91.105" />
-      <line id="46,60" x1="149.376" y1="105.417" x2="148.703" y2="90.432" />
-      <line id="47,59" x1="164.361" y1="104.744" x2="163.688" y2="89.759" />
-      <line id="48,58" x1="179.345" y1="104.071" x2="178.673" y2="89.086" />
-      <line id="49,57" x1="194.330" y1="103.398" x2="193.657" y2="88.413" />
-    </g>
-    <g style="font-family: SansSerif" transform="translate(-4.6, 4)" id="seq">
-      <text x="112.164" y="-10.084">A</text>
-      <text x="111.491" y="4.901">A</text>
-      <text x="110.818" y="19.886">G</text>
-      <text x="110.145" y="34.870">G</text>
-      <text x="109.472" y="49.855">G</text>
-      <text x="108.799" y="64.840">C</text>
-      <text x="108.126" y="79.825">U</text>
-      <text x="92.018" y="81.598">U</text>
-      <text x="79.209" y="90.125">A</text>
-      <text x="72.157" y="102.876">G</text>
-      <text x="57.292" y="100.862">C</text>
-      <text x="42.428" y="98.849">U</text>
-      <text x="27.564" y="96.835">U</text>
-      <text x="16.740" y="84.993">A</text>
-      <text x="0.744" y="86.216">A</text>
-      <text x="-8.154" y="99.565">U</text>
-      <text x="-3.128" y="114.801">U</text>
-      <text x="11.966" y="120.235">A</text>
-      <text x="25.550" y="111.700">A</text>
-      <text x="40.415" y="113.713">A</text>
-      <text x="55.279" y="115.727">G</text>
-      <text x="70.143" y="117.740">U</text>
-      <text x="74.909" y="130.778">G</text>
-      <text x="85.025" y="140.285">G</text>
-      <text x="81.034" y="154.745">C</text>
-      <text x="77.044" y="169.204">U</text>
-      <text x="73.053" y="183.663">G</text>
-      <text x="69.063" y="198.123">A</text>
-      <text x="54.767" y="204.460">U</text>
-      <text x="47.936" y="218.527">U</text>
-      <text x="51.795" y="233.681">U</text>
-      <text x="64.522" y="242.767">G</text>
-      <text x="80.108" y="241.495">C</text>
-      <text x="91.193" y="230.465">G</text>
-      <text x="92.544" y="214.886">U</text>
-      <text x="83.522" y="202.113">U</text>
-      <text x="87.513" y="187.654">C</text>
-      <text x="91.503" y="173.195">A</text>
-      <text x="95.494" y="158.735">G</text>
-      <text x="99.484" y="144.276">U</text>
-      <text x="110.578" y="143.482">U</text>
-      <text x="120.992" y="138.597">G</text>
-      <text x="129.225" y="130.028">A</text>
-      <text x="133.985" y="118.727">U</text>
-      <text x="134.391" y="106.090">G</text>
-      <text x="149.376" y="105.417">C</text>
-      <text x="164.361" y="104.744">A</text>
-      <text x="179.345" y="104.071">G</text>
-      <text x="194.330" y="103.398">A</text>
-      <text x="204.775" y="115.035">G</text>
-      <text x="220.264" y="117.185">U</text>
-      <text x="233.484" y="108.832">G</text>
-      <text x="238.193" y="93.920">G</text>
-      <text x="232.166" y="79.490">G</text>
-      <text x="218.251" y="72.356">G</text>
-      <text x="203.017" y="75.886">U</text>
-      <text x="193.657" y="88.413">U</text>
-      <text x="178.673" y="89.086">U</text>
-      <text x="163.688" y="89.759">U</text>
-      <text x="148.703" y="90.432">G</text>
-      <text x="133.718" y="91.105">C</text>
-      <text x="123.111" y="80.498">A</text>
-      <text x="123.784" y="65.513">G</text>
-      <text x="124.457" y="50.528">U</text>
-      <text x="125.130" y="35.543">C</text>
-      <text x="125.803" y="20.559">C</text>
-      <text x="126.476" y="5.574">U</text>
-      <text x="127.149" y="-9.411">U</text>
-      <text x="130.202" y="-28.551">A</text>
-    </g>
-  </g>
-</svg>
diff -r c8f5229645ef -r 6cd432abcf8e test-data/mitos2_NC_012920.gff
--- a/test-data/mitos2_NC_012920.gff	Wed Mar 01 22:38:41 2023 +0000
+++ b/test-data/mitos2_NC_012920.gff	Wed Dec 10 23:30:17 2025 +0000
@@ -1,54 +1,56 @@
-NC_012920\tmitfi\tncRNA_gene\t577\t647\t\.\t\+\t\.\tID=gene_trnF;gene_id=trnF
-NC_012920\tmitfi\ttRNA\t577\t647\t\.\t\+\t\.\tID=transcript_trnF;Parent=gene_trnF;gene_id=trnF
-NC_012920\tmitfi\texon\t577\t647\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnF;Name=trnF
-NC_012920\tmitfi\tncRNA_gene\t648\t1601\t\.\t\+\t\.\tID=gene_rrnS;gene_id=rrnS
-NC_012920\tmitfi\trRNA\t648\t1601\t\.\t\+\t\.\tID=transcript_rrnS;Parent=gene_rrnS;gene_id=rrnS
+##gff-version 3
+#!gff-spec-version 1\.21
+NC_012920\tmitos\tregion\t1\t16569\t\.\t\+\t\.\tID=NC_012920:1\.\.16569;Is_circular=True;Name=NC_012920;genome=mitochondrion;mol_type=genomic DNA
+NC_012920\tmitfi\tncRNA_gene\t577\t647\t\.\t\+\t\.\tID=gene_trnF;Name=trnF;gene_id=trnF
+NC_012920\tmitfi\ttRNA\t577\t647\t\.\t\+\t\.\tID=transcript_trnF\(gaa\);Name=trnF\(gaa\);Parent=gene_trnF\(gaa\);gene_id=trnF\(gaa\)
+NC_012920\tmitfi\texon\t577\t647\t9\.999999747378752e-06\t\+\t\.\tParent=transcript_trnF;Name=trnF
+NC_012920\tmitfi\tncRNA_gene\t648\t1601\t\.\t\+\t\.\tID=gene_rrnS;Name=rrnS;gene_id=rrnS
+NC_012920\tmitfi\trRNA\t648\t1601\t\.\t\+\t\.\tID=transcript_rrnS;Name=rrnS;Parent=gene_rrnS;gene_id=rrnS
 NC_012920\tmitfi\texon\t648\t1601\t0\.0\t\+\t\.\tParent=transcript_rrnS;Name=rrnS
-NC_012920\tmitfi\tncRNA_gene\t3230\t3304\t\.\t\+\t\.\tID=gene_trnL2;gene_id=trnL2
-NC_012920\tmitfi\ttRNA\t3230\t3304\t\.\t\+\t\.\tID=transcript_trnL2;Parent=gene_trnL2;gene_id=trnL2
-NC_012920\tmitfi\texon\t3230\t3304\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnL2;Name=trnL2
-NC_012920\tmitfi\tncRNA_gene\t4263\t4331\t\.\t\+\t\.\tID=gene_trnI;gene_id=trnI
-NC_012920\tmitfi\ttRNA\t4263\t4331\t\.\t\+\t\.\tID=transcript_trnI;Parent=gene_trnI;gene_id=trnI
-NC_012920\tmitfi\texon\t4263\t4331\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnI;Name=trnI
-NC_012920\tmitfi\tncRNA_gene\t4402\t4469\t\.\t\+\t\.\tID=gene_trnM;gene_id=trnM
-NC_012920\tmitfi\ttRNA\t4402\t4469\t\.\t\+\t\.\tID=transcript_trnM;Parent=gene_trnM;gene_id=trnM
-NC_012920\tmitfi\texon\t4402\t4469\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnM;Name=trnM
-NC_012920\tmitfi\tncRNA_gene\t5587\t5655\t\.\t-\t\.\tID=gene_trnA;gene_id=trnA
-NC_012920\tmitfi\ttRNA\t5587\t5655\t\.\t-\t\.\tID=transcript_trnA;Parent=gene_trnA;gene_id=trnA
-NC_012920\tmitfi\texon\t5587\t5655\t[-0-9.e]+\t-\t\.\tParent=transcript_trnA;Name=trnA
-NC_012920\tmitfi\tncRNA_gene\t5657\t5729\t\.\t-\t\.\tID=gene_trnN;gene_id=trnN
-NC_012920\tmitfi\ttRNA\t5657\t5729\t\.\t-\t\.\tID=transcript_trnN;Parent=gene_trnN;gene_id=trnN
-NC_012920\tmitfi\texon\t5657\t5729\t[-0-9.e]+\t-\t\.\tParent=transcript_trnN;Name=trnN
-NC_012920\tmitfi\tncRNA_gene\t5826\t5891\t\.\t-\t\.\tID=gene_trnY;gene_id=trnY
-NC_012920\tmitfi\ttRNA\t5826\t5891\t\.\t-\t\.\tID=transcript_trnY;Parent=gene_trnY;gene_id=trnY
-NC_012920\tmitfi\texon\t5826\t5891\t[-0-9.e]+\t-\t\.\tParent=transcript_trnY;Name=trnY
-NC_012920\tmitfi\tncRNA_gene\t7446\t7514\t\.\t-\t\.\tID=gene_trnS2;gene_id=trnS2
-NC_012920\tmitfi\ttRNA\t7446\t7514\t\.\t-\t\.\tID=transcript_trnS2;Parent=gene_trnS2;gene_id=trnS2
-NC_012920\tmitfi\texon\t7446\t7514\t[-0-9.e]+\t-\t\.\tParent=transcript_trnS2;Name=trnS2
-NC_012920\tmitfi\tncRNA_gene\t7518\t7585\t\.\t\+\t\.\tID=gene_trnD;gene_id=trnD
-NC_012920\tmitfi\ttRNA\t7518\t7585\t\.\t\+\t\.\tID=transcript_trnD;Parent=gene_trnD;gene_id=trnD
-NC_012920\tmitfi\texon\t7518\t7585\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnD;Name=trnD
-NC_012920\tmitfi\tncRNA_gene\t8295\t8364\t\.\t\+\t\.\tID=gene_trnK;gene_id=trnK
-NC_012920\tmitfi\ttRNA\t8295\t8364\t\.\t\+\t\.\tID=transcript_trnK;Parent=gene_trnK;gene_id=trnK
-NC_012920\tmitfi\texon\t8295\t8364\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnK;Name=trnK
-NC_012920\tmitfi\tncRNA_gene\t10405\t10469\t\.\t\+\t\.\tID=gene_trnR;gene_id=trnR
-NC_012920\tmitfi\ttRNA\t10405\t10469\t\.\t\+\t\.\tID=transcript_trnR;Parent=gene_trnR;gene_id=trnR
-NC_012920\tmitfi\texon\t10405\t10469\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnR;Name=trnR
-NC_012920\tmitfi\tncRNA_gene\t12138\t12206\t\.\t\+\t\.\tID=gene_trnH;gene_id=trnH
-NC_012920\tmitfi\ttRNA\t12138\t12206\t\.\t\+\t\.\tID=transcript_trnH;Parent=gene_trnH;gene_id=trnH
-NC_012920\tmitfi\texon\t12138\t12206\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnH;Name=trnH
-NC_012920\tmitfi\tncRNA_gene\t12266\t12336\t\.\t\+\t\.\tID=gene_trnL1;gene_id=trnL1
-NC_012920\tmitfi\ttRNA\t12266\t12336\t\.\t\+\t\.\tID=transcript_trnL1;Parent=gene_trnL1;gene_id=trnL1
-NC_012920\tmitfi\texon\t12266\t12336\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnL1;Name=trnL1
-NC_012920\tmitos\tgene\t14149\t14670\t\.\t-\t\.\tID=gene_nad6;gene_id=nad6
-NC_012920\tmitos\tmRNA\t14149\t14670\t\.\t-\t\.\tID=transcript_nad6;Parent=gene_nad6;gene_id=nad6
-NC_012920\tmitos\texon\t14149\t14670\t[-0-9.e]+\t-\t2\.0\tParent=transcript_nad6;Name=nad6
-NC_012920\tmitfi\tncRNA_gene\t14674\t14742\t\.\t-\t\.\tID=gene_trnE;gene_id=trnE
-NC_012920\tmitfi\ttRNA\t14674\t14742\t\.\t-\t\.\tID=transcript_trnE;Parent=gene_trnE;gene_id=trnE
-NC_012920\tmitfi\texon\t14674\t14742\t[-0-9.e]+\t-\t\.\tParent=transcript_trnE;Name=trnE
-NC_012920\tmitfi\tncRNA_gene\t15888\t15953\t\.\t\+\t\.\tID=gene_trnT;gene_id=trnT
-NC_012920\tmitfi\ttRNA\t15888\t15953\t\.\t\+\t\.\tID=transcript_trnT;Parent=gene_trnT;gene_id=trnT
-NC_012920\tmitfi\texon\t15888\t15953\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnT;Name=trnT
-NC_012920\tmitfi\tncRNA_gene\t15956\t16023\t\.\t-\t\.\tID=gene_trnP;gene_id=trnP
-NC_012920\tmitfi\ttRNA\t15956\t16023\t\.\t-\t\.\tID=transcript_trnP;Parent=gene_trnP;gene_id=trnP
-NC_012920\tmitfi\texon\t15956\t16023\t[-0-9.e]+\t-\t\.\tParent=transcript_trnP;Name=trnP
+NC_012920\tmitfi\tncRNA_gene\t3230\t3304\t\.\t\+\t\.\tID=gene_trnL2;Name=trnL2;gene_id=trnL2
+NC_012920\tmitfi\ttRNA\t3230\t3304\t\.\t\+\t\.\tID=transcript_trnL2\(taa\);Name=trnL2\(taa\);Parent=gene_trnL2\(taa\);gene_id=trnL2\(taa\)
+NC_012920\tmitfi\texon\t3230\t3304\t2\.100000074278796e-06\t\+\t\.\tParent=transcript_trnL2;Name=trnL2
+NC_012920\tmitfi\tncRNA_gene\t4263\t4331\t\.\t\+\t\.\tID=gene_trnI;Name=trnI;gene_id=trnI
+NC_012920\tmitfi\ttRNA\t4263\t4331\t\.\t\+\t\.\tID=transcript_trnI\(gat\);Name=trnI\(gat\);Parent=gene_trnI\(gat\);gene_id=trnI\(gat\)
+NC_012920\tmitfi\texon\t4263\t4331\t6\.000000212225132e-07\t\+\t\.\tParent=transcript_trnI;Name=trnI
+NC_012920\tmitfi\tncRNA_gene\t4402\t4469\t\.\t\+\t\.\tID=gene_trnM;Name=trnM;gene_id=trnM
+NC_012920\tmitfi\ttRNA\t4402\t4469\t\.\t\+\t\.\tID=transcript_trnM\(cat\);Name=trnM\(cat\);Parent=gene_trnM\(cat\);gene_id=trnM\(cat\)
+NC_012920\tmitfi\texon\t4402\t4469\t0\.0034000000450760126\t\+\t\.\tParent=transcript_trnM;Name=trnM
+NC_012920\tmitfi\tncRNA_gene\t5587\t5655\t\.\t-\t\.\tID=gene_trnA;Name=trnA;gene_id=trnA
+NC_012920\tmitfi\ttRNA\t5587\t5655\t\.\t-\t\.\tID=transcript_trnA\(tgc\);Name=trnA\(tgc\);Parent=gene_trnA\(tgc\);gene_id=trnA\(tgc\)
+NC_012920\tmitfi\texon\t5587\t5655\t0\.0017999999690800905\t-\t\.\tParent=transcript_trnA;Name=trnA
+NC_012920\tmitfi\tncRNA_gene\t5657\t5729\t\.\t-\t\.\tID=gene_trnN;Name=trnN;gene_id=trnN
+NC_012920\tmitfi\ttRNA\t5657\t5729\t\.\t-\t\.\tID=transcript_trnN\(gtt\);Name=trnN\(gtt\);Parent=gene_trnN\(gtt\);gene_id=trnN\(gtt\)
+NC_012920\tmitfi\texon\t5657\t5729\t0\.07400000095367432\t-\t\.\tParent=transcript_trnN;Name=trnN
+NC_012920\tmitfi\tncRNA_gene\t5826\t5891\t\.\t-\t\.\tID=gene_trnY;Name=trnY;gene_id=trnY
+NC_012920\tmitfi\ttRNA\t5826\t5891\t\.\t-\t\.\tID=transcript_trnY\(gta\);Name=trnY\(gta\);Parent=gene_trnY\(gta\);gene_id=trnY\(gta\)
+NC_012920\tmitfi\texon\t5826\t5891\t4\.2000001634662394e-15\t-\t\.\tParent=transcript_trnY;Name=trnY
+NC_012920\tmitfi\tncRNA_gene\t7446\t7514\t\.\t-\t\.\tID=gene_trnS2;Name=trnS2;gene_id=trnS2
+NC_012920\tmitfi\ttRNA\t7446\t7514\t\.\t-\t\.\tID=transcript_trnS2\(tga\);Name=trnS2\(tga\);Parent=gene_trnS2\(tga\);gene_id=trnS2\(tga\)
+NC_012920\tmitfi\texon\t7446\t7514\t0\.03999999910593033\t-\t\.\tParent=transcript_trnS2;Name=trnS2
+NC_012920\tmitfi\tncRNA_gene\t7518\t7585\t\.\t\+\t\.\tID=gene_trnD;Name=trnD;gene_id=trnD
+NC_012920\tmitfi\ttRNA\t7518\t7585\t\.\t\+\t\.\tID=transcript_trnD\(gtc\);Name=trnD\(gtc\);Parent=gene_trnD\(gtc\);gene_id=trnD\(gtc\)
+NC_012920\tmitfi\texon\t7518\t7585\t0\.0007099999929778278\t\+\t\.\tParent=transcript_trnD;Name=trnD
+NC_012920\tmitfi\tncRNA_gene\t8295\t8364\t\.\t\+\t\.\tID=gene_trnK;Name=trnK;gene_id=trnK
+NC_012920\tmitfi\ttRNA\t8295\t8364\t\.\t\+\t\.\tID=transcript_trnK\(ttt\);Name=trnK\(ttt\);Parent=gene_trnK\(ttt\);gene_id=trnK\(ttt\)
+NC_012920\tmitfi\texon\t8295\t8364\t0\.03799999877810478\t\+\t\.\tParent=transcript_trnK;Name=trnK
+NC_012920\tmitfi\tncRNA_gene\t10405\t10469\t\.\t\+\t\.\tID=gene_trnR;Name=trnR;gene_id=trnR
+NC_012920\tmitfi\ttRNA\t10405\t10469\t\.\t\+\t\.\tID=transcript_trnR\(tcg\);Name=trnR\(tcg\);Parent=gene_trnR\(tcg\);gene_id=trnR\(tcg\)
+NC_012920\tmitfi\texon\t10405\t10469\t0\.005100000184029341\t\+\t\.\tParent=transcript_trnR;Name=trnR
+NC_012920\tmitfi\tncRNA_gene\t12138\t12206\t\.\t\+\t\.\tID=gene_trnH;Name=trnH;gene_id=trnH
+NC_012920\tmitfi\ttRNA\t12138\t12206\t\.\t\+\t\.\tID=transcript_trnH\(gtg\);Name=trnH\(gtg\);Parent=gene_trnH\(gtg\);gene_id=trnH\(gtg\)
+NC_012920\tmitfi\texon\t12138\t12206\t1\.9999999949504854e-06\t\+\t\.\tParent=transcript_trnH;Name=trnH
+NC_012920\tmitfi\tncRNA_gene\t12266\t12336\t\.\t\+\t\.\tID=gene_trnL1;Name=trnL1;gene_id=trnL1
+NC_012920\tmitfi\ttRNA\t12266\t12336\t\.\t\+\t\.\tID=transcript_trnL1\(tag\);Name=trnL1\(tag\);Parent=gene_trnL1\(tag\);gene_id=trnL1\(tag\)
+NC_012920\tmitfi\texon\t12266\t12336\t0\.026000000536441803\t\+\t\.\tParent=transcript_trnL1;Name=trnL1
+NC_012920\tmitos\tgene\t14149\t14670\t\.\t-\t\.\tID=gene_nad6;Name=nad6;gene_id=nad6
+NC_012920\tmitos\texon\t14149\t14670\t39\.7\t-\t0\tParent=transcript_nad6;Name=nad6
+NC_012920\tmitfi\tncRNA_gene\t14674\t14742\t\.\t-\t\.\tID=gene_trnE;Name=trnE;gene_id=trnE
+NC_012920\tmitfi\ttRNA\t14674\t14742\t\.\t-\t\.\tID=transcript_trnE\(ttc\);Name=trnE\(ttc\);Parent=gene_trnE\(ttc\);gene_id=trnE\(ttc\)
+NC_012920\tmitfi\texon\t14674\t14742\t0\.03200000151991844\t-\t\.\tParent=transcript_trnE;Name=trnE
+NC_012920\tmitfi\tncRNA_gene\t15888\t15953\t\.\t\+\t\.\tID=gene_trnT;Name=trnT;gene_id=trnT
+NC_012920\tmitfi\ttRNA\t15888\t15953\t\.\t\+\t\.\tID=transcript_trnT\(tgt\);Name=trnT\(tgt\);Parent=gene_trnT\(tgt\);gene_id=trnT\(tgt\)
+NC_012920\tmitfi\texon\t15888\t15953\t0\.0012000000569969416\t\+\t\.\tParent=transcript_trnT;Name=trnT
+NC_012920\tmitfi\tncRNA_gene\t15956\t16023\t\.\t-\t\.\tID=gene_trnP;Name=trnP;gene_id=trnP
+NC_012920\tmitfi\ttRNA\t15956\t16023\t\.\t-\t\.\tID=transcript_trnP\(tgg\);Name=trnP\(tgg\);Parent=gene_trnP\(tgg\);gene_id=trnP\(tgg\)
+NC_012920\tmitfi\texon\t15956\t16023\t0\.005200000014156103\t-\t\.\tParent=transcript_trnP;Name=trnP
diff -r c8f5229645ef -r 6cd432abcf8e test-data/mitos2_NC_012920.seq
--- a/test-data/mitos2_NC_012920.seq	Wed Mar 01 22:38:41 2023 +0000
+++ b/test-data/mitos2_NC_012920.seq	Wed Dec 10 23:30:17 2025 +0000
@@ -1,72 +1,72 @@
 >Feature NC_012920
-576	646	gene
+577	647	gene
 			gene	trnF(gaa)
-576	646	tRNA
+577	647	tRNA
 			product	tRNA-PHE
-647	1600	gene
-647	1600	rRNA
+			gene	rrnS
+648	1601	rRNA
 			product	s-rRNA
-3229	3303	gene
+3230	3304	gene
 			gene	trnL2(taa)
-3229	3303	tRNA
+3230	3304	tRNA
 			product	tRNA-LEU2
-4262	4330	gene
+4263	4331	gene
 			gene	trnI(gat)
-4262	4330	tRNA
+4263	4331	tRNA
 			product	tRNA-ILE
-4401	4468	gene
+4402	4469	gene
 			gene	trnM(cat)
-4401	4468	tRNA
+4402	4469	tRNA
 			product	tRNA-MET
-5654	5586	gene
+5655	5587	gene
 			gene	trnA(tgc)
-5654	5586	tRNA
+5655	5587	tRNA
 			product	tRNA-ALA
-5728	5656	gene
+5729	5657	gene
 			gene	trnN(gtt)
-5728	5656	tRNA
+5729	5657	tRNA
 			product	tRNA-ASN
-5890	5825	gene
+5891	5826	gene
 			gene	trnY(gta)
-5890	5825	tRNA
+5891	5826	tRNA
 			product	tRNA-TYR
-7513	7445	gene
+7514	7446	gene
 			gene	trnS2(tga)
-7513	7445	tRNA
+7514	7446	tRNA
 			product	tRNA-SER2
-7517	7584	gene
+7518	7585	gene
 			gene	trnD(gtc)
-7517	7584	tRNA
+7518	7585	tRNA
 			product	tRNA-ASP
-8294	8363	gene
+8295	8364	gene
 			gene	trnK(ttt)
-8294	8363	tRNA
+8295	8364	tRNA
 			product	tRNA-LYS
-10404	10468	gene
+10405	10469	gene
 			gene	trnR(tcg)
-10404	10468	tRNA
+10405	10469	tRNA
 			product	tRNA-ARG
-12137	12205	gene
+12138	12206	gene
 			gene	trnH(gtg)
-12137	12205	tRNA
+12138	12206	tRNA
 			product	tRNA-HIS
-12265	12335	gene
+12266	12336	gene
 			gene	trnL1(tag)
-12265	12335	tRNA
+12266	12336	tRNA
 			product	tRNA-LEU1
-14669	14148	gene
+14670	14149	gene
 			gene	nad6
-14669	14148	CDS
+14670	14149	CDS
 			product	NADH dehydrogenase subunit 6
-14741	14673	gene
+14742	14674	gene
 			gene	trnE(ttc)
-14741	14673	tRNA
+14742	14674	tRNA
 			product	tRNA-GLU
-15887	15952	gene
+15888	15953	gene
 			gene	trnT(tgt)
-15887	15952	tRNA
+15888	15953	tRNA
 			product	tRNA-THR
-16022	15955	gene
+16023	15956	gene
 			gene	trnP(tgg)
-16022	15955	tRNA
+16023	15956	tRNA
 			product	tRNA-PRO
diff -r c8f5229645ef -r 6cd432abcf8e test-data/mitos2_NC_012920_ncrna.pdf
Binary file test-data/mitos2_NC_012920_ncrna.pdf has changed
diff -r c8f5229645ef -r 6cd432abcf8e test-data/mitos2_NC_012920_prot.pdf
Binary file test-data/mitos2_NC_012920_prot.pdf has changed