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Add ToolDistillator #5967

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Apr 30, 2024
Merged

Add ToolDistillator #5967

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3956353
Add ToolDistillator
clsiguret Apr 25, 2024
49ceab1
Change ToolDistillator command
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c840f09
Apply suggestions from code review for ToolDistillator
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Apply suggestions from code review for ToolDistillator
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Apply suggestions from code review for ToolDistillator
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a58618f
Remove files not used
clsiguret Apr 25, 2024
4fe5480
Remove tooldistillator_summary.json because size file was too large
clsiguret Apr 25, 2024
e72ec95
Update tooldistillator_summarize.xml: planemo test was not working wi…
clsiguret Apr 25, 2024
79fa47d
New release 0.8.4.1 ToolDistillator in Bioconda
clsiguret Apr 26, 2024
596a21c
Error planemo test: table in section Help of tooldistillator.xml had …
clsiguret Apr 26, 2024
abf6da7
Change test-data and tests for Bakta because the files were too large
clsiguret Apr 26, 2024
39d39fc
Change test-data and tests for Kraken2 because the files were too large
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b877947
Remove test-data html for MultiQC because the files were too large an…
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Apply suggestions from code review
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560f36a
Change double-quotes to single-quotes
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Remove synthax: diff to None
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Remove empty or not used files
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a190a4d
Change tests in XML files + remove None and str term
clsiguret Apr 26, 2024
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22 changes: 22 additions & 0 deletions tools/tooldistillator/.shed.yml
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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"
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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
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
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38 changes: 38 additions & 0 deletions tools/tooldistillator/macro.xml
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<?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>
25 changes: 25 additions & 0 deletions tools/tooldistillator/test-data/abricate/report.tsv
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#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]
Empty file added tools/tooldistillator/test-data/abricate_logfile.txt
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this is empty, is it needed or should it be removed?

Empty file.
95 changes: 95 additions & 0 deletions tools/tooldistillator/test-data/bakta/bakta.json
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{
"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"
}
}
}
4 changes: 4 additions & 0 deletions tools/tooldistillator/test-data/bakta/bakta_aminoacid.faa
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>IHHALP_00005 hypothetical protein
MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD
>IHHALP_00010 hypothetical protein
MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI
36 changes: 36 additions & 0 deletions tools/tooldistillator/test-data/bakta/bakta_annotation.gff3
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##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
8 changes: 8 additions & 0 deletions tools/tooldistillator/test-data/bakta/bakta_annotation.tsv
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# 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
24 changes: 24 additions & 0 deletions tools/tooldistillator/test-data/bakta/bakta_contigs_sequences.fna
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>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
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