Add ToolDistillator (galaxyproject#5967)

* Add ToolDistillator * Change ToolDistillator command * Apply suggestions from code review for ToolDistillator Co-authored-by: Bérénice Batut <[email protected]> * Apply suggestions from code review for ToolDistillator Co-authored-by: Bérénice Batut <[email protected]> * Apply suggestions from code review for ToolDistillator Co-authored-by: Bérénice Batut <[email protected]> * Apply suggestions from code review for ToolDistillator Co-authored-by: Bérénice Batut <[email protected]> * Remove files not used * Remove tooldistillator_summary.json because size file was too large * Update tooldistillator_summarize.xml: planemo test was not working with "" around input_files/ * New release 0.8.4.1 ToolDistillator in Bioconda * Error planemo test: table in section Help of tooldistillator.xml had invalid text * Change test-data and tests for Bakta because the files were too large * Change test-data and tests for Kraken2 because the files were too large * Remove test-data html for MultiQC because the files were too large and not used by test * Apply suggestions from code review Co-authored-by: Björn Grüning <[email protected]> * Change double-quotes to single-quotes * Remove synthax: diff to None * Remove empty or not used files * Change tests in XML files + remove None and str term --------- Co-authored-by: Bérénice Batut <[email protected]> Co-authored-by: Björn Grüning <[email protected]>
bebatut · Apr 30, 2024 · 491c6fc · 491c6fc
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diff --git a/tools/tooldistillator/.shed.yml b/tools/tooldistillator/.shed.yml
@@ -0,0 +1,17 @@
+name: tooldistillator
+owner: iuc
+long_description: |
+  ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files
+categories:
+- Sequence Analysis
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator
+homepage_url: https://gitlab.com/ifb-elixirfr/abromics/tooldistillator
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "{{ tool_name }}: Extract information from tool output(s) to JSON and/or aggregate several JSON reports"
+suite:
+  name: "suite_tooldistillator"
+  description: "Tool to extract and aggregate information from different tool outputs to JSON parsable files"
+  long_description: |
+    ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files
diff --git a/tools/tooldistillator/macro.xml b/tools/tooldistillator/macro.xml
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.8.4.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+    <xml name="version_command">
+        <version_command><![CDATA[tooldistillator --version]]></version_command>
+    </xml>
+    <xml name="analysis_software_version">
+        <param argument="--analysis_software_version" type="text" optional="true" label="Analysis software version"/>
+    </xml>
+    <xml name="reference_database_version">
+        <param argument="--reference_database_version" type="text" optional="true" label="Database software version"/>
+    </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">tooldistillator</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">tooldistillator</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.5281/zenodo.8282656</citation>
+        </citations>
+    </xml>
+    <xml name="element_assert" token_name="" token_text="">
+        <element name="@NAME@">
+            <assert_contents>
+                <has_text text="@TEXT@"/>
+                <yield/>
+            </assert_contents>
+        </element>
+    </xml>
+</macros>
diff --git a/tools/tooldistillator/test-data/abricate/report.tsv b/tools/tooldistillator/test-data/abricate/report.tsv
@@ -0,0 +1,25 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00002	142975	143985	+	bopD	1-1011/1011	===============	0/0	100.00	98.91	vfdb	NP_814691	(bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00003	7884	11111	-	fss3	1-3228/3228	===============	0/0	100.00	99.38	vfdb	NP_815578	(fss3) Enterococcus faecalis surface protein Fss3 fibrinogen binding protein [Fibrinogen binding protein (AI273)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00003	162314	163240	+	efaA	1-927/927	===============	0/0	100.00	99.89	vfdb	NP_815739	(efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00006	33703	37014	+	ebpA	1-3312/3312	===============	0/0	100.00	99.49	vfdb	NP_814821	(ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00006	37018	38448	+	ebpB	1-1431/1431	===============	0/0	100.00	99.30	vfdb	NP_814822	(ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00006	38445	40328	+	ebpC	1-1878/1878	========/======	1/6	100.00	98.99	vfdb	NP_814823	(ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00006	40422	41276	+	srtC	1-855/855	===============	0/0	100.00	99.30	vfdb	NP_814824	(srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00006	44356	46374	+	ace	1-2025/2025	========/======	2/6	99.70	96.74	vfdb	NP_814829	(ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00010	49447	50301	-	sprE	1-855/855	===============	0/0	100.00	98.36	vfdb	NP_815515	(sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00010	50350	51882	-	gelE	1-1533/1533	===============	0/0	100.00	98.96	vfdb	NP_815516	(gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00010	52117	53200	-	fsrC	261-1344/1344	..=============	0/0	80.65	99.26	vfdb	NP_815517	(fsrC) histidine kinase putative [Fsr (VF0360)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	14420	15232	-	cpsK	1-813/813	===============	0/0	100.00	99.88	vfdb	NP_816131	(cpsK) ABC transporter permease protein [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	15232	16575	-	cpsJ	1-1344/1344	===============	0/0	100.00	98.96	vfdb	NP_816132	(cpsJ) ABC transporter ATP-binding protein [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	16601	17739	-	cpsI	1-1140/1140	========/======	1/1	99.91	98.33	vfdb	NP_816133	(cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	17798	18196	-	cpsH	1-399/399	===============	0/0	100.00	97.49	vfdb	NP_816134	(cpsH) lipoprotein [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	18214	20666	-	cpsG	1-2454/2454	========/======	1/1	99.96	99.51	vfdb	NP_816135	(cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	20736	23245	-	cpsE	1-2510/2511	===============	0/0	99.96	99.40	vfdb	NP_816137	(cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	23315	24781	-	cpsD	1-1467/1467	===============	0/0	100.00	98.91	vfdb	NP_816138	(cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	24800	25969	-	cpsC	1-1170/1170	===============	0/0	100.00	99.57	vfdb	NP_816139	(cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	26443	27243	-	cpsB	1-801/801	===============	0/0	100.00	99.50	vfdb	NP_816140	(cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	27240	28055	-	cpsA	1-816/816	===============	0/0	100.00	99.51	vfdb	NP_816141	(cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00018	36270	40580	-	fss2	1-4305/4956	========/=====.	11/22	86.70	92.92	vfdb	NP_816151	(fss2) Enterococcus faecalis surface protein Fss2 fibrinogen binding protein [Fibrinogen binding protein (AI272)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00023	14087	18004	+	prgB/asc10	1-3918/3918	========/======	2/4	99.95	94.26	vfdb	NP_817031	(prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583]	
+/storage/scratch/piemari/60579281/abricate/10_Enterococcus_faecalis_S17_L001.fasta	contig00042	2539	8502	-	fss1	1-5964/5964	===============	0/0	100.00	98.31	vfdb	NP_813892	(fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583]	
diff --git a/tools/tooldistillator/test-data/bakta/bakta.json b/tools/tooldistillator/test-data/bakta/bakta.json
@@ -0,0 +1,95 @@
+{
+    "genome": {
+        "genus": null,
+        "species": null,
+        "strain": null,
+        "complete": true,
+        "gram": "?",
+        "translation_table": 11
+    },
+    "stats": {
+        "no_sequences": 1,
+        "size": 1330,
+        "gc": 0.4518796992481203,
+        "n_ratio": 0.0,
+        "n50": 1330,
+        "coding_ratio": 0.6203007518796992
+    },
+    "features": [
+        {
+            "type": "cds",
+            "contig": "contig_1",
+            "start": 413,
+            "stop": 736,
+            "strand": "+",
+            "frame": 2,
+            "gene": null,
+            "product": "hypothetical protein",
+            "db_xrefs": [],
+            "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG",
+            "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD",
+            "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e",
+            "start_type": "ATG",
+            "rbs_motif": "GGAG/GAGG",
+            "hypothetical": true,
+            "genes": [],
+            "seq_stats": {
+                "molecular_weight": 12072.90819999999,
+                "isoelectric_point": 10.367886161804197
+            },
+            "id": "IHHALPPJCH_1",
+            "locus": "IHHALP_00005"
+        },
+        {
+            "type": "cds",
+            "contig": "contig_1",
+            "start": 971,
+            "stop": 141,
+            "strand": "-",
+            "frame": 1,
+            "gene": null,
+            "product": "hypothetical protein",
+            "db_xrefs": [],
+            "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA",
+            "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI",
+            "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584",
+            "start_type": "ATG",
+            "rbs_motif": "AGGA/GGAG/GAGG",
+            "edge": true,
+            "hypothetical": true,
+            "genes": [],
+            "seq_stats": {
+                "molecular_weight": 18866.325799999995,
+                "isoelectric_point": 7.696590614318848
+            },
+            "id": "IHHALPPJCH_2",
+            "locus": "IHHALP_00010"
+        }
+    ],
+    "sequences": [
+        {
+            "id": "contig_1",
+            "description": "[gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1]",
+            "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG",
+            "length": 1330,
+            "complete": true,
+            "type": "plasmid",
+            "topology": "circular",
+            "simple_id": "contig_1",
+            "orig_id": "NC_002127.1",
+            "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence",
+            "name": "unnamed1"
+        }
+    ],
+    "run": {
+        "start": "2024-02-11 00:24:53",
+        "end": "2024-02-11 00:25:06"
+    },
+    "version": {
+        "bakta": "1.9.2",
+        "db": {
+            "version": "5.0",
+            "type": "full"
+        }
+    }
+}
diff --git a/tools/tooldistillator/test-data/bakta/bakta_aminoacid.faa b/tools/tooldistillator/test-data/bakta/bakta_aminoacid.faa
@@ -0,0 +1,4 @@
+>IHHALP_00005 hypothetical protein
+MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD
+>IHHALP_00010 hypothetical protein
+MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI
diff --git a/tools/tooldistillator/test-data/bakta/bakta_annotation.gff3 b/tools/tooldistillator/test-data/bakta/bakta_annotation.gff3
@@ -0,0 +1,36 @@
+##gff-version 3
+##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
+# Annotated with Bakta
+# Software: v1.9.2
+# Database: v5.0, full
+# DOI: 10.1099/mgen.0.000685
+# URL: github.com/oschwengers/bakta
+##sequence-region contig_1 1 1330
+contig_1	Bakta	region	1	1330	.	+	.	ID=contig_1;Name=contig_1;Is_circular=true
+contig_1	Prodigal	CDS	413	736	.	+	0	ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein
+contig_1	Prodigal	CDS	971	1471	.	-	0	ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein
+##FASTA
+>contig_1
+TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC
+GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC
+AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG
+TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT
+TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT
+GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC
+CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA
+ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA
+AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT
+ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA
+AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA
+CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG
+GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT
+AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA
+TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC
+AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC
+TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA
+GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT
+CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT
+TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA
+AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC
+TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG
+CTTCTATTTG
diff --git a/tools/tooldistillator/test-data/bakta/bakta_annotation.tsv b/tools/tooldistillator/test-data/bakta/bakta_annotation.tsv
@@ -0,0 +1,8 @@
+# Annotated with Bakta
+# Software: v1.9.2
+# Database: v5.0, full
+# DOI: 10.1099/mgen.0.000685
+# URL: github.com/oschwengers/bakta
+#Sequence Id	Type	Start	Stop	Strand	Locus Tag	Gene	Product	DbXrefs
+contig_1	cds	413	736	+	IHHALP_00005		hypothetical protein	
+contig_1	cds	971	141	-	IHHALP_00010		hypothetical protein	
diff --git a/tools/tooldistillator/test-data/bakta/bakta_contigs_sequences.fna b/tools/tooldistillator/test-data/bakta/bakta_contigs_sequences.fna
@@ -0,0 +1,24 @@
+>contig_1 [gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1]
+TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC
+GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC
+AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG
+TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT
+TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT
+GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC
+CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA
+ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA
+AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT
+ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA
+AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA
+CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG
+GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT
+AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA
+TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC
+AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC
+TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA
+GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT
+CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT
+TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA
+AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC
+TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG
+CTTCTATTTG