# HG changeset patch
# User iuc
# Date 1677710377 0
# Node ID 033755194fe9486d079f0384e3c0f6d4ad52a406
# Parent  624606f7c99659bc3a5eaa8805175e1aaac2c6e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484

diff -r 624606f7c996 -r 033755194fe9 mitos2.xml
--- a/mitos2.xml	Tue Jun 14 17:16:16 2022 +0000
+++ b/mitos2.xml	Wed Mar 01 22:39:37 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<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>
@@ -6,12 +6,11 @@
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS2</token>
-    <token name="@TOOL_VERSION@">2.0.6</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">2.1.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
-    <requirement type="package" version="3.0">zip</requirement>
   </requirements>
   <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
   <command detect_errors="aggressive"><![CDATA[
@@ -51,20 +50,17 @@
 #if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
   --noplots
 #end if
+#if "raw" in str($addoutputs).split(','):
+  --zip
+#end if
 
 #if "missing" in $addoutputs:
     > outdir/missing.txt
 #end if
-
-#if "raw" in str($addoutputs).split(','):
-    && zip -9 -y -r output.zip outdir/ > /dev/null
-#end if
   ]]></command>
   <inputs>
     <param argument="--input" label="Sequence" type="data" format="fasta" help="A single sequence in fasta formated sequence">
-      <options options_filter_attribute="metadata.sequences">
-        <filter type="add_value" value="1"/>
-      </options>
+      <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/>
     </param> 
     <param argument="--code" label="Genetic code" type="select">
       <option value="2">Vertebrate (2)</option>
@@ -154,15 +150,11 @@
     <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
       <filter>"ncRNA_plot" in str(addoutputs)</filter>
     </data>
-    <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots">
-      <discover_datasets pattern="(?P&lt;name&gt;.+)\.ps" format="ps" directory="outdir/plots" />
-      <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter>
-    </collection>-->
     <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
       <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
       <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
     </collection>
-    <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
+    <data name="rawout" format="zip" from_work_dir="outdir.zip" label="${tool.name} on ${on_string}: raw data">
       <filter>"raw" in str(addoutputs)</filter>
     </data>
     <data name="missing_genes" format="txt" from_work_dir="outdir/missing.txt" label="${tool.name} on ${on_string}: missing genes">
@@ -175,7 +167,7 @@
       <param name="input" value="NC_012920.fasta"/>
       <param name="code" value="2"/>
       <param name="refseqver" value="mitos2-refdata" />
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
+      <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
       <assert_command>
         <has_text text="--code 2"/>
         <has_text text="--finovl 50"/>
@@ -202,7 +194,11 @@
       <param name="input" value="NC_012920.fasta"/>
       <param name="code" value="5"/>
       <param name="refseqver" value="mitos2-refdata" />
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
+      <output name="bedout" ftype="bed">
+        <assert_contents>
+          <has_n_lines n="8"/>
+        </assert_contents>
+      </output>
       <section name="advanced">
         <param name="featuretypes" value="prot,trna,rrna,intron,oril,orih"/>
         <param name="finovl" value="49"/>
@@ -252,9 +248,13 @@
         <param name="maxrrnaovl" value="49"/>
       </section>
       <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots,raw"/>
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
-      <output name="mitoout" file="mitos2_NC_012920.mitos" ftype="tabular"/>
-      <output name="gffout" file="mitos2_NC_012920.gff" ftype="gff"/>
+      <output name="bedout" ftype="bed">
+        <assert_contents>
+          <has_n_lines n="18"/>
+        </assert_contents>
+      </output>
+      <output name="mitoout" file="mitos2_NC_012920.mitos" compare="re_match" ftype="tabular"/>
+      <output name="gffout" file="mitos2_NC_012920.gff" compare="re_match" ftype="gff"/>
       <output name="seqout" file="mitos2_NC_012920.seq" ftype="txt"/>
       <output name="faa" file="mitos2_NC_012920.faa" ftype="fasta"/>
       <output name="fas" file="mitos2_NC_012920.fas" ftype="fasta"/>
@@ -263,7 +263,7 @@
       <output name="ncRNA_plot_out" file="mitos2_NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
       <output name="rawout" ftype="zip">
         <assert_contents>
-          <has_archive_member path=".*/result.bed"/>
+          <has_archive_member path="result.bed"/>
         </assert_contents>
       </output>
       <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="17"/>
@@ -299,8 +299,12 @@
       <param name="code" value="2"/>
       <param name="refseqver" value="mitos2-refdata" />
       <param name="addoutputs" value="bed,missing"/>
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
-      <output name="missing_genes" file="missing_genes.txt" ftype="txt"/>
+      <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>
       <assert_command>
         <has_text text="--code 2"/>
         <has_text text="--finovl 50"/>
diff -r 624606f7c996 -r 033755194fe9 test-data/missing_genes.txt
--- a/test-data/missing_genes.txt	Tue Jun 14 17:16:16 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-missing:cox2 cox3 trnS2 cox1 trnL1 nad3 nad2 nad1 nad5 nad4 atp8 atp6 trnS1 rrnL trnP trnK trnM trnN trnA trnC trnD trnE trnF trnG cob nad4l trnQ trnR trnT trnV trnW 
diff -r 624606f7c996 -r 033755194fe9 test-data/mitos2_NC_012920.bed
--- a/test-data/mitos2_NC_012920.bed	Tue Jun 14 17:16:16 2022 +0000
+++ b/test-data/mitos2_NC_012920.bed	Wed Mar 01 22:39:37 2023 +0000
@@ -1,6 +1,6 @@
-NC_012920	647	1601	rrnS	0.0	+
-NC_012920	3229	3304	trnL2(taa)	2.10000007428e-06	+
-NC_012920	4262	4331	trnI(gat)	6.00000021223e-07	+
-NC_012920	5825	5891	trnY(gta)	4.20000016347e-15	-
-NC_012920	12137	12206	trnH(gtg)	1.99999999495e-06	+
-NC_012920	14148	14673	nad6	876137.8	-
+NC_012920\t647\t1601\trrnS\t[-0-9.e]+\t\+
+NC_012920\t3229\t3304\ttrnL2\(taa\)\t[-0-9.e]+\t\+
+NC_012920\t4262\t4331\ttrnI\(gat\)\t[-0-9.e]+\t\+
+NC_012920\t5825\t5891\ttrnY\(gta\)\t[-0-9.e]+\t-
+NC_012920\t12137\t12206\ttrnH\(gtg\)\t[-0-9.e]+\t\+
+NC_012920\t14148\t14673\tnad6\t[-0-9.e]+\t-
diff -r 624606f7c996 -r 033755194fe9 test-data/mitos2_NC_012920.gff
--- a/test-data/mitos2_NC_012920.gff	Tue Jun 14 17:16:16 2022 +0000
+++ b/test-data/mitos2_NC_012920.gff	Wed Mar 01 22:39:37 2023 +0000
@@ -1,54 +1,54 @@
-NC_012920	mitfi	ncRNA_gene	577	647	.	+	.	ID=gene_trnF;gene_id=trnF
-NC_012920	mitfi	tRNA	577	647	.	+	.	ID=transcript_trnF;Parent=gene_trnF;gene_id=trnF
-NC_012920	mitfi	exon	577	647	9.99999974738e-06	+	.	Parent=transcript_trnF;Name=trnF
-NC_012920	mitfi	ncRNA_gene	648	1601	.	+	.	ID=gene_rrnS;gene_id=rrnS
-NC_012920	mitfi	rRNA	648	1601	.	+	.	ID=transcript_rrnS;Parent=gene_rrnS;gene_id=rrnS
-NC_012920	mitfi	exon	648	1601	0.0	+	.	Parent=transcript_rrnS;Name=rrnS
-NC_012920	mitfi	ncRNA_gene	3230	3304	.	+	.	ID=gene_trnL2;gene_id=trnL2
-NC_012920	mitfi	tRNA	3230	3304	.	+	.	ID=transcript_trnL2;Parent=gene_trnL2;gene_id=trnL2
-NC_012920	mitfi	exon	3230	3304	2.10000007428e-06	+	.	Parent=transcript_trnL2;Name=trnL2
-NC_012920	mitfi	ncRNA_gene	4263	4331	.	+	.	ID=gene_trnI;gene_id=trnI
-NC_012920	mitfi	tRNA	4263	4331	.	+	.	ID=transcript_trnI;Parent=gene_trnI;gene_id=trnI
-NC_012920	mitfi	exon	4263	4331	6.00000021223e-07	+	.	Parent=transcript_trnI;Name=trnI
-NC_012920	mitfi	ncRNA_gene	4402	4469	.	+	.	ID=gene_trnM;gene_id=trnM
-NC_012920	mitfi	tRNA	4402	4469	.	+	.	ID=transcript_trnM;Parent=gene_trnM;gene_id=trnM
-NC_012920	mitfi	exon	4402	4469	0.00340000004508	+	.	Parent=transcript_trnM;Name=trnM
-NC_012920	mitfi	ncRNA_gene	5587	5655	.	-	.	ID=gene_trnA;gene_id=trnA
-NC_012920	mitfi	tRNA	5587	5655	.	-	.	ID=transcript_trnA;Parent=gene_trnA;gene_id=trnA
-NC_012920	mitfi	exon	5587	5655	0.00179999996908	-	.	Parent=transcript_trnA;Name=trnA
-NC_012920	mitfi	ncRNA_gene	5657	5729	.	-	.	ID=gene_trnN;gene_id=trnN
-NC_012920	mitfi	tRNA	5657	5729	.	-	.	ID=transcript_trnN;Parent=gene_trnN;gene_id=trnN
-NC_012920	mitfi	exon	5657	5729	0.0740000009537	-	.	Parent=transcript_trnN;Name=trnN
-NC_012920	mitfi	ncRNA_gene	5826	5891	.	-	.	ID=gene_trnY;gene_id=trnY
-NC_012920	mitfi	tRNA	5826	5891	.	-	.	ID=transcript_trnY;Parent=gene_trnY;gene_id=trnY
-NC_012920	mitfi	exon	5826	5891	4.20000016347e-15	-	.	Parent=transcript_trnY;Name=trnY
-NC_012920	mitfi	ncRNA_gene	7446	7514	.	-	.	ID=gene_trnS2;gene_id=trnS2
-NC_012920	mitfi	tRNA	7446	7514	.	-	.	ID=transcript_trnS2;Parent=gene_trnS2;gene_id=trnS2
-NC_012920	mitfi	exon	7446	7514	0.0399999991059	-	.	Parent=transcript_trnS2;Name=trnS2
-NC_012920	mitfi	ncRNA_gene	7518	7585	.	+	.	ID=gene_trnD;gene_id=trnD
-NC_012920	mitfi	tRNA	7518	7585	.	+	.	ID=transcript_trnD;Parent=gene_trnD;gene_id=trnD
-NC_012920	mitfi	exon	7518	7585	0.000709999992978	+	.	Parent=transcript_trnD;Name=trnD
-NC_012920	mitfi	ncRNA_gene	8295	8364	.	+	.	ID=gene_trnK;gene_id=trnK
-NC_012920	mitfi	tRNA	8295	8364	.	+	.	ID=transcript_trnK;Parent=gene_trnK;gene_id=trnK
-NC_012920	mitfi	exon	8295	8364	0.0379999987781	+	.	Parent=transcript_trnK;Name=trnK
-NC_012920	mitfi	ncRNA_gene	10405	10469	.	+	.	ID=gene_trnR;gene_id=trnR
-NC_012920	mitfi	tRNA	10405	10469	.	+	.	ID=transcript_trnR;Parent=gene_trnR;gene_id=trnR
-NC_012920	mitfi	exon	10405	10469	0.00510000018403	+	.	Parent=transcript_trnR;Name=trnR
-NC_012920	mitfi	ncRNA_gene	12138	12206	.	+	.	ID=gene_trnH;gene_id=trnH
-NC_012920	mitfi	tRNA	12138	12206	.	+	.	ID=transcript_trnH;Parent=gene_trnH;gene_id=trnH
-NC_012920	mitfi	exon	12138	12206	1.99999999495e-06	+	.	Parent=transcript_trnH;Name=trnH
-NC_012920	mitfi	ncRNA_gene	12266	12336	.	+	.	ID=gene_trnL1;gene_id=trnL1
-NC_012920	mitfi	tRNA	12266	12336	.	+	.	ID=transcript_trnL1;Parent=gene_trnL1;gene_id=trnL1
-NC_012920	mitfi	exon	12266	12336	0.0260000005364	+	.	Parent=transcript_trnL1;Name=trnL1
-NC_012920	mitos	gene	14149	14670	.	-	.	ID=gene_nad6;gene_id=nad6
-NC_012920	mitos	mRNA	14149	14670	.	-	.	ID=transcript_nad6;Parent=gene_nad6;gene_id=nad6
-NC_012920	mitos	exon	14149	14670	39.7	-	2.0	Parent=transcript_nad6;Name=nad6
-NC_012920	mitfi	ncRNA_gene	14674	14742	.	-	.	ID=gene_trnE;gene_id=trnE
-NC_012920	mitfi	tRNA	14674	14742	.	-	.	ID=transcript_trnE;Parent=gene_trnE;gene_id=trnE
-NC_012920	mitfi	exon	14674	14742	0.0320000015199	-	.	Parent=transcript_trnE;Name=trnE
-NC_012920	mitfi	ncRNA_gene	15888	15953	.	+	.	ID=gene_trnT;gene_id=trnT
-NC_012920	mitfi	tRNA	15888	15953	.	+	.	ID=transcript_trnT;Parent=gene_trnT;gene_id=trnT
-NC_012920	mitfi	exon	15888	15953	0.001200000057	+	.	Parent=transcript_trnT;Name=trnT
-NC_012920	mitfi	ncRNA_gene	15956	16023	.	-	.	ID=gene_trnP;gene_id=trnP
-NC_012920	mitfi	tRNA	15956	16023	.	-	.	ID=transcript_trnP;Parent=gene_trnP;gene_id=trnP
-NC_012920	mitfi	exon	15956	16023	0.00520000001416	-	.	Parent=transcript_trnP;Name=trnP
+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
+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
diff -r 624606f7c996 -r 033755194fe9 test-data/mitos2_NC_012920.mitos
--- a/test-data/mitos2_NC_012920.mitos	Tue Jun 14 17:16:16 2022 +0000
+++ b/test-data/mitos2_NC_012920.mitos	Wed Mar 01 22:39:37 2023 +0000
@@ -1,18 +1,18 @@
-NC_012920	tRNA	trnF	mitfi	576	646	1	9.99999974738e-06	31.3	GAA	34	.	.	(((((((..((((.........)))).(.(((.......))).)....(((.........)))))))))).
-NC_012920	rRNA	rrnS	mitfi	647	1600	1	0.0	769.2	-	None	.	.	...(((((.......))))).((((((.(((.((((((((....(((.(((..(......)......(((.......(((.(..(((.....)))..).)))....(((.(...............)..)))...(..((...)).)...)))...((....)).....))))))........((((...(((((....))))).)))).)).)))))).....((((((((................)))..............))))).))).))))))....((((......((((.(((((...............(((((((.....(((.(((((((......)))).))).))).............((....))))))))).....))).)).))))....((((((...((...((((.........))))...))))))))..........(......................))))).((.......((((....)))).....))........((((.((((((((.......(((((..((((((((((...((((........))))........(((((((.......((.((..((((((((.(....((....(((.....)))...........)).....(((....))).....).).)))...))))))))....)))))))..)).)))))))).....((((.....))))..........(((((((.......)))))))..........))))).....(((((((.........)))))))...........)))))))))).))..............((((((................................................))))))................((((((((((....)))))))))).......
-NC_012920	tRNA	trnL2	mitfi	3229	3303	1	2.10000007428e-06	34.1	TAA	35	.	.	(((((((..((..............)).((((.........)))).....(((((.......)))))))))))).
-NC_012920	tRNA	trnI	mitfi	4262	4330	1	6.00000021223e-07	36.3	GAT	29	.	.	(((((((..(((......))).(((((.......))))).....(((.(.......).)))))))))).
-NC_012920	tRNA	trnM	mitfi	4401	4468	1	0.00340000004508	21.1	CAT	30	.	.	((((.((..((((.....)))).(((((.......)))))....(..((......))..))).)))).
-NC_012920	tRNA	trnA	mitfi	5586	5654	-1	0.00179999996908	22.2	TGC	30	.	.	(((((((..((((.....)))).(((((.......)))))....(((((.......)))))))))))).
-NC_012920	tRNA	trnN	mitfi	5656	5728	-1	0.0740000009537	15.7	GTT	33	.	.	(((((((..(((..........))).(((((.......))))).....(((((.......)))))))))))).
-NC_012920	tRNA	trnY	mitfi	5825	5890	-1	4.20000016347e-15	69.2	GTA	29	.	.	(((((((..(((......))).(((((.......)))))....(((((.....)))))))))))).
-NC_012920	tRNA	trnS2	mitfi	7445	7513	-1	0.0399999991059	16.8	TGA	30	.	.	(((((((((((.......)))).(((((.......)))))....(((((.......)))))))))))).
-NC_012920	tRNA	trnD	mitfi	7517	7584	1	0.000709999992978	23.9	GTC	30	.	.	(((((((..((((.....)))).(((((.......)))))....(((((......)))))))))))).
-NC_012920	tRNA	trnK	mitfi	8294	8363	1	0.0379999987781	16.9	TTT	28	.	.	(((((((..((((...)))).(((((.......))))).....(((((.........)))))))))))).
-NC_012920	tRNA	trnR	mitfi	10404	10468	1	0.00510000018403	20.4	TCG	30	.	.	(((((.(..((((.....)))).(((((.......)))))....(((((...)))))).))))).
-NC_012920	tRNA	trnH	mitfi	12137	12205	1	1.99999999495e-06	34.2	GTG	30	.	.	(((((((..((((.....)))).(((((.......)))))....((.((.......)).))))))))).
-NC_012920	tRNA	trnL1	mitfi	12265	12335	1	0.0260000005364	17.6	TAG	32	.	.	(((((((..((((.......)))).((((.........))))....(((((.......)))))))))))).
-NC_012920	gene	nad6	mitos	14148	14669	-1	39.7	.	-	-	.	.	.
-NC_012920	tRNA	trnE	mitfi	14673	14741	-1	0.0320000015199	17.2	TTC	30	.	.	(((((((..((((.....)))).(((((.......)))))....(((((.......)))))))))))).
-NC_012920	tRNA	trnT	mitfi	15887	15952	1	0.001200000057	23.0	TGT	31	.	.	(((((((..((((......)))).((.(.........).))....(((((...)))))))))))).
-NC_012920	tRNA	trnP	mitfi	15955	16022	-1	0.00520000001416	20.4	TGG	31	.	.	(((((((..((((......)))).(((((.......)))))....(((((.....)))))))))))).
+NC_012920\ttRNA\ttrnF\tmitfi\t576\t646\t1\t[-0-9.e]+\t31\.3\tGAA\t34\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\.\(\.\(\(\(\.\.\.\.\.\.\.\)\)\)\.\)\.\.\.\.\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\trRNA\trrnS\tmitfi\t647\t1600\t1\t[-0-9.e]+\t769\.2\t-\tNone\t\.\t\.\t\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\(\(\(\(\(\(\.\(\(\(\.\(\(\(\(\(\(\(\(\.\.\.\.\(\(\(\.\(\(\(\.\.\(\.\.\.\.\.\.\)\.\.\.\.\.\.\(\(\(\.\.\.\.\.\.\.\(\(\(\.\(\.\.\(\(\(\.\.\.\.\.\)\)\)\.\.\)\.\)\)\)\.\.\.\.\(\(\(\.\(\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\)\.\.\)\)\)\.\.\.\(\.\.\(\(\.\.\.\)\)\.\)\.\.\.\)\)\)\.\.\.\(\(\.\.\.\.\)\)\.\.\.\.\.\)\)\)\)\)\)\.\.\.\.\.\.\.\.\(\(\(\(\.\.\.\(\(\(\(\(\.\.\.\.\)\)\)\)\)\.\)\)\)\)\.\)\)\.\)\)\)\)\)\)\.\.\.\.\.\(\(\(\(\(\(\(\(\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\)\)\)\.\.\.\.\.\.\.\.\.\.\.\.\.\.\)\)\)\)\)\.\)\)\)\.\)\)\)\)\)\)\.\.\.\.\(\(\(\(\.\.\.\.\.\.\(\(\(\(\.\(\(\(\(\(\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\(\(\(\(\(\(\(\.\.\.\.\.\(\(\(\.\(\(\(\(\(\(\(\.\.\.\.\.\.\)\)\)\)\.\)\)\)\.\)\)\)\.\.\.\.\.\.\.\.\.\.\.\.\.\(\(\.\.\.\.\)\)\)\)\)\)\)\)\)\.\.\.\.\.\)\)\)\.\)\)\.\)\)\)\)\.\.\.\.\(\(\(\(\(\(\.\.\.\(\(\.\.\.\(\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\.\.\.\)\)\)\)\)\)\)\)\.\.\.\.\.\.\.\.\.\.\(\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\)\)\)\)\)\.\(\(\.\.\.\.\.\.\.\(\(\(\(\.\.\.\.\)\)\)\)\.\.\.\.\.\)\)\.\.\.\.\.\.\.\.\(\(\(\(\.\(\(\(\(\(\(\(\(\.\.\.\.\.\.\.\(\(\(\(\(\.\.\(\(\(\(\(\(\(\(\(\(\.\.\.\(\(\(\(\.\.\.\.\.\.\.\.\)\)\)\)\.\.\.\.\.\.\.\.\(\(\(\(\(\(\(\.\.\.\.\.\.\.\(\(\.\(\(\.\.\(\(\(\(\(\(\(\(\.\(\.\.\.\.\(\(\.\.\.\.\(\(\(\.\.\.\.\.\)\)\)\.\.\.\.\.\.\.\.\.\.\.\)\)\.\.\.\.\.\(\(\(\.\.\.\.\)\)\)\.\.\.\.\.\)\.\)\.\)\)\)\.\.\.\)\)\)\)\)\)\)\)\.\.\.\.\)\)\)\)\)\)\)\.\.\)\)\.\)\)\)\)\)\)\)\)\.\.\.\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\.\.\.\.\.\.\.\.\.\(\(\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\)\)\.\.\.\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\(\(\(\(\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\)\)\)\.\.\.\.\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\.\)\)\.\.\.\.\.\.\.\.\.\.\.\.\.\.\(\(\(\(\(\(\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\)\)\)\)\)\)\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\(\(\(\(\(\(\(\(\(\(\.\.\.\.\)\)\)\)\)\)\)\)\)\)\.\.\.\.\.\.\.
+NC_012920\ttRNA\ttrnL2\tmitfi\t3229\t3303\t1\t[-0-9.e]+\t34\.1\tTAA\t35\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\.\.\.\.\.\.\.\.\.\.\.\.\.\.\)\)\.\(\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnI\tmitfi\t4262\t4330\t1\t[-0-9.e]+\t36\.3\tGAT\t29\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\.\.\.\.\.\.\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\(\(\(\.\(\.\.\.\.\.\.\.\)\.\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnM\tmitfi\t4401\t4468\t1\t[-0-9.e]+\t21\.1\tCAT\t30\t\.\t\.\t\(\(\(\(\.\(\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\.\.\(\(\.\.\.\.\.\.\)\)\.\.\)\)\)\.\)\)\)\)\.
+NC_012920\ttRNA\ttrnA\tmitfi\t5586\t5654\t-1\t[-0-9.e]+\t22\.2\tTGC\t30\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnN\tmitfi\t5656\t5728\t-1\t[-0-9.e]+\t15\.7\tGTT\t33\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\.\.\.\.\.\.\.\.\.\.\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnY\tmitfi\t5825\t5890\t-1\t[-0-9.e]+\t69\.2\tGTA\t29\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\.\.\.\.\.\.\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnS2\tmitfi\t7445\t7513\t-1\t[-0-9.e]+\t16\.8\tTGA\t30\t\.\t\.\t\(\(\(\(\(\(\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnD\tmitfi\t7517\t7584\t1\t[-0-9.e]+\t23\.9\tGTC\t30\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnK\tmitfi\t8294\t8363\t1\t[-0-9.e]+\t16\.9\tTTT\t28\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnR\tmitfi\t10404\t10468\t1\t[-0-9.e]+\t20\.4\tTCG\t30\t\.\t\.\t\(\(\(\(\(\.\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\)\)\)\)\)\)\.\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnH\tmitfi\t12137\t12205\t1\t[-0-9.e]+\t34\.2\tGTG\t30\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\.\(\(\.\.\.\.\.\.\.\)\)\.\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnL1\tmitfi\t12265\t12335\t1\t[-0-9.e]+\t17\.6\tTAG\t32\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\.\(\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\tgene\tnad6\tmitos\t14148\t14669\t-1\t39\.7\t\.\t-\t-\t\.\t\.\t\.
+NC_012920\ttRNA\ttrnE\tmitfi\t14673\t14741\t-1\t[-0-9.e]+\t17\.2\tTTC\t30\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnT\tmitfi\t15887\t15952\t1\t[-0-9.e]+\t23\.0\tTGT\t31\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\.\)\)\)\)\.\(\(\.\(\.\.\.\.\.\.\.\.\.\)\.\)\)\.\.\.\.\(\(\(\(\(\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.
+NC_012920\ttRNA\ttrnP\tmitfi\t15955\t16022\t-1\t[-0-9.e]+\t20\.4\tTGG\t31\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\.\)\)\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\(\(\(\(\(\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\)\)\.