| Previous changeset 6:9424de64bfa8 (2019-12-11) Next changeset 8:53f50adcb78e (2020-11-28) |
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Commit message:
"planemo upload for repository https://github.com/phac-nml/mob-suite commit 814769a7d86fa4ca552e93f8d707412e9ba23b1b" |
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modified:
README.md mob_recon.xml mob_typer.xml |
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added:
test-data/Ecoli_strain_KV7_complete_LT795502.fasta |
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removed:
test-data/contig_report.txt |
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| diff -r 9424de64bfa8 -r 822575bf359f README.md --- a/README.md Wed Dec 11 19:17:11 2019 -0500 +++ b/README.md Fri Jun 05 13:02:15 2020 -0400 |
| [ |
| @@ -1,7 +1,7 @@ # MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies -These are Galaxy wrappers for [MOB-Suite](https://github.com/phac-nml/mob-suite): a set of tools designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies. This wrapper allows to conveniently run all these tools on a Galaxy instance. Also coupling MOB-Suite tools with other AMR tools via workflows allows to obtain both mobilome and resistome valuable information. +These are Galaxy wrappers for [MOB-Suite](https://github.com/phac-nml/mob-suite): a set of tools designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies. This wrapper allows to conveniently run all these tools on a Galaxy instance. The `workflows` folder contains a workflow coupling MOB-Suite with other AMR detection tools for both mobilome and resistome analyses. For more information please refer to https://github.com/phac-nml/mob-suite |
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| diff -r 9424de64bfa8 -r 822575bf359f mob_recon.xml --- a/mob_recon.xml Wed Dec 11 19:17:11 2019 -0500 +++ b/mob_recon.xml Fri Jun 05 13:02:15 2020 -0400 |
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| b'@@ -1,7 +1,7 @@\n-<tool id="mob_recon" name="MOB-Recon" version="2.0.5+galaxy0">\n+<tool id="mob_recon" name="MOB-Recon" version="3.0.0">\n <description>Type contigs and extract plasmid sequences</description>\n <requirements>\n- <requirement type="package" version="2.0.5">mob_suite</requirement>\n+ <requirement type="package" version="3.0.0">mob_suite</requirement>\n </requirements>\n <version_command>mob_recon --version</version_command>\n <command detect_errors="exit_code">\n@@ -12,17 +12,51 @@\n #set $named_input = re.sub(r\'(\\s|\\(|\\)|:|!)\', \'_\', str($input.element_identifier)+\'.fasta\')\n ln -s \'$input\' \'$named_input\' &&\n \n- mob_recon --num_threads \\${GALAXY_SLOTS:-4} --infile \'${named_input}\'\n- #if str($adv_param.unicycler_contigs) == "True":\n+\n+ mob_recon --num_threads \\${GALAXY_SLOTS:-4} --infile \'${named_input}\' --run_typer\n+\n+ #if $adv_param.unicycler_contigs:\n --unicycler_contigs \n #end if \n- #if str($adv_param.run_circlator) == "True":\n- --run_circlator \n+\n+ #if $adv_param.run_overhang:\n+ --run_overhang\n #end if \n- #if str($adv_param.min_length_condition.min_length_param) == "True":\n- --min_length \'${adv_param.min_length_condition.min_length_value}\'\n- #end if \n- --run_typer --min_rep_evalue \'${adv_param.min_rep_evalue}\'\n+ \n+ #if $adv_param.debug:\n+ --debug\n+ #end if\n+\n+ #if $adv_param.plasmid_db\n+ --plasmid_db \'$adv_param.plasmid_db\'\n+ #end if\n+\n+ #if $adv_param.plasmid_mash_db\n+ --plasmid_mash_db \'$adv_param.plasmid_mash_db\'\n+ #end if\n+\n+ #if $adv_param.plasmid_meta\n+ --plasmid_meta \'$adv_param.plasmid_meta\'\n+ #end if\n+\n+ #if $adv_param.repetitive_mask\n+ --repetitive_mask \'$adv_param.repetitive_mask\'\n+ #end if\n+\n+ #if $adv_param.plasmid_mob\n+ --plasmid_mob \'$adv_param.plasmid_mob\'\n+ #end if\n+ \n+ #if $adv_param.plasmid_mpf\n+ --plasmid_mpf \'$adv_param.plasmid_mpf\'\n+ #end if\n+\n+ #if $adv_param.plasmid_orit\n+ --plasmid_orit \'$adv_param.plasmid_orit\'\n+ #end if\n+\n+ --min_length \'${adv_param.min_length}\' \n+ --min_rep_evalue \'${adv_param.min_rep_evalue}\'\n --min_rep_evalue \'${adv_param.min_rep_evalue}\'\n --min_mob_evalue \'${adv_param.min_mob_evalue}\'\n --min_con_evalue \'${adv_param.min_con_evalue}\'\n@@ -30,6 +64,11 @@\n --min_mob_ident \'${adv_param.min_mob_ident}\'\n --min_con_ident \'${adv_param.min_con_ident}\'\n --min_rpp_ident \'${adv_param.min_rpp_ident}\'\n+\n+ --min_rep_cov \'${adv_param.min_rep_cov}\'\n+ --min_mob_cov \'${adv_param.min_mob_cov}\'\n+ --min_con_cov \'${adv_param.min_con_cov}\'\n+ --min_rpp_cov \'${adv_param.min_rpp_cov}\'\n --outdir \'outdir\' &&\n mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)\n ]]> \n@@ -37,38 +76,38 @@\n <inputs>\n <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>\n <section name="adv_param" title="Advanced parameters" expanded="False">\n- <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">\n- <option value="True">Yes</option>\n- <option value="False">No</option>\n- </param>\n- <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">\n- <option value="True">Yes</option>\n- <option value="False">No</option>\n- </param>\n- <conditional name="min_length_condition">\n- <param name="min_length_param" label="Minimum length of contigs to process" type="select" value="False">\n- <option value="False">No</option>\n- <option value="True">Yes</option>\n- </param> \n- <when value="True">\n- <param name="min_length_value" type="integer" value="500" min="50"/> \n- </when> \n- <when value="False"/>\n- </conditional> \n+ <param name="unicycler_contigs" type'..b'ity for repetitive elements" type="integer" min="0" max="100" value="80"/>\n+\n+ <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/>\n+ <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/>\n+ <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer" min="0" max="100" value="60"/>\n+ <param name="min_rpp_cov" label="Minimum percentage coverage of contigs by repetitive elements" type="integer" min="0" max="100" value="80"/>\n+\n+ <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/>\n+ <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="MASH sketch of the reference plasmids database"/>\n+ <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help=""/>\n+ <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help=""/>\n+ <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help=""/>\n+ <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help=""/>\n+ <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help=""/>\n+ <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help=""/>\n </section> \n </inputs>\n <outputs>\n <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/> \n- <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${input.element_identifier}: Repetitive elements BLAST report"/>\n- <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>\n+ <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_results.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>\n <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/>\n <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids">\n <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />\n@@ -76,14 +115,24 @@\n </outputs>\n <tests>\n <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta"/>\n+ <param name="input" value="Ecoli_strain_KV7_complete_LT795502.fasta" ftype="fasta"/>\n <section name="adv_param">\n <param name="unicycler_contigs" value="True"/>\n- <param name="run_circlator" value="True"/>\n+ <param name="run_overhang" value="True"/>\n </section>\n <output name="contig_report">\n <assert_contents>\n- <has_text text="NC_019097"/>\n+ <has_text text="chromosome"/>\n+ <has_text text="plasmid"/>\n+ <has_text text="IncHI1A"/>\n+ <has_text text="IncN"/>\n+ </assert_contents>\n+ </output>\n+ <output name="mobtyper_aggregate_report">\n+ <assert_contents>\n+ <has_text text="conjugative"/>\n+ <has_text text="Gammaproteobacteria"/>\n+ <has_text text="223020"/>\n </assert_contents>\n </output>\n </test>\n' |
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| diff -r 9424de64bfa8 -r 822575bf359f mob_typer.xml --- a/mob_typer.xml Wed Dec 11 19:17:11 2019 -0500 +++ b/mob_typer.xml Fri Jun 05 13:02:15 2020 -0400 |
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| b'@@ -1,153 +1,110 @@\n-<tool id="mob_typer" name="MOB-Typer" version="2.0.5+galaxy0">\n+<tool id="mob_typer" name="MOB-Typer" version="3.0.0">\n <description>Get the plasmid type and mobility given its sequence</description>\n <requirements>\n- <requirement type="package" version="2.0.5">mob_suite</requirement>\n+ <requirement type="package" version="3.0.0">mob_suite</requirement>\n </requirements>\n <version_command>mob_typer --version</version_command>\n <command detect_errors="exit_code">\n <![CDATA[\n ln -s \'${input}\' \'${input.name}\' &&\n mob_typer --num_threads \\${GALAXY_SLOTS:-4} --infile \'${input.name}\'\n- ${host_range_detailed}\n+\n+\n+ #if $adv_param.multi\n+ --multi\n+ #end if \n+\n --min_rep_evalue \'$adv_param.min_rep_evalue_value\'\n --min_mob_evalue \'$adv_param.min_mob_evalue_value\'\n --min_con_evalue \'$adv_param.min_con_evalue_value\'\n- --min_ori_evalue \'$adv_param.min_ori_evalue_value\'\n- --min_mpf_evalue \'$adv_param.min_mpf_evalue\'\n+ --min_length \'$adv_param.min_length\'\n --min_rep_ident \'$adv_param.min_rep_ident\'\n --min_mob_ident \'$adv_param.min_mob_ident\'\n- --min_ori_ident \'$adv_param.min_ori_ident\'\n- --min_mpf_ident \'$adv_param.min_mpf_ident\'\n- --outdir \'outdir\';\n+\n+ --min_con_ident \'$adv_param.min_con_ident\'\n+ --min_rep_cov \'$adv_param.min_rep_cov\'\n+ --min_mob_cov \'$adv_param.min_mob_cov\'\n+ --min_con_cov \'$adv_param.min_con_cov\'\n+ --min_overlap \'$adv_param.min_overlap\'\n+ \n+ #if $adv_param.plasmid_db\n+ --plasmid_db \'$adv_param.plasmid_db\'\n+ #end if\n+\n+\n+ #if $adv_param.plasmid_mash_db\n+ --plasmid_mash_db \'$adv_param.plasmid_mash_db\'\n+ #end if\n+\n+ #if $adv_param.plasmid_meta\n+ --plasmid_meta \'$adv_param.plasmid_meta\'\n+ #end if\n+\n+ #if $adv_param.repetitive_mask\n+ --repetitive_mask \'$adv_param.repetitive_mask\'\n+ #end if\n+\n+ #if $adv_param.plasmid_mob\n+ --plasmid_mob \'$adv_param.plasmid_mob\'\n+ #end if\n+ \n+ #if $adv_param.plasmid_mpf\n+ --plasmid_mpf \'$adv_param.plasmid_mpf\'\n+ #end if\n+\n+ #if $adv_param.plasmid_orit\n+ --plasmid_orit \'$adv_param.plasmid_orit\'\n+ #end if\n+\n+ #if $adv_param.debug\n+ --debug\n+ #end if\n+\n+ --out_file plasmid_report.txt;\n+\n ]]>\n </command>\n <inputs>\n <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>\n- <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="true" label="Perform detailed host range analysis" />\n <section name="adv_param" title="Advanced parameters" expanded="False">\n+ <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independant plasmid?" />\n <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> \n <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> \n <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> \n- <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/>\n- <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/>\n+ <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify"/> \n <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>\n <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>\n- <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/>\n- <param name='..b'entifier}" format="tabular" />\n </outputs>\n <tests>\n <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="False" />\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta"/>\n <output name="plasmid_report">\n <assert_contents>\n- <has_text text="000145__HE610900_00001"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="True" />\n- <output name="refseq_hostrange_phylogeny_tree">\n- <assert_contents>\n- <has_text text="(624:1,984897:1)"/> \n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="True" />\n- <output name="literature_hostrange_phylogeny_tree">\n- <assert_contents>\n- <has_text text="(90371:1,611:1,28144:1)"/> \n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="True" />\n- <output name="refseq_hostrange_ascii_tree">\n- <assert_contents>\n- <has_text text="order, Enterobacterales"/>\n- <has_text text="family, Enterobacteriaceae"/>\n- <has_text text="genus, Shigella"/>\n- <has_text text="species, Escherichia coli"/>\n- <has_text text="genus, Serratia"/>\n- <has_text text="species, Serratia marcescens"/>\n- <has_text text="species, Klebsiella pneumoniae"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="True" />\n- <output name="literature_hostrange_ascii_tree">\n- <assert_contents>\n- <has_text text="family, Enterobacteriaceae"/>\n- <has_text text="species, Escherichia coli"/>\n- <has_text text="species, Klebsiella pneumoniae"/>\n- <has_text text="subspecies, Salmonella enterica subsp. enterica"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="True" />\n- <output name="literature_report">\n- <assert_contents>\n- <has_text text="IncI1"/>\n- <has_text text="R64"/>\n- <has_text text="pHNRD174"/>\n- <has_text text="pKHSB1"/>\n- <has_text text="pCTXM1-MU2"/>\n+ <has_text text="KJ484639"/>\n+ <has_text text="MOBP"/>\n+ <has_text text="NC_019097"/>\n+ <has_text text="conjugative"/>\n+ <has_text text="AA474"/>\n+ <has_text text="AI614"/>\n <has_text_matching expression="family\\tEnterobacteriaceae"/>\n- <has_text_matching expression="order\\tEnterobacteriales"/>\n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="True" />\n- <output name="refseq_hostrange_report">\n- <assert_contents>\n- <has_text text="IncI1"/>\n- <has_text text="Enterobacterales"/> \n- </assert_contents>\n- </output>\n- </test>\n- <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n- <param name="host_range_detailed" value="True" />\n- <output name="refseq_hostrange_phylostats">\n- <assert_contents>\n- <has_line_matching expression="rank\\tsci_name\\tdb_hits\\tconvergance_rank\\tconvergance_sci_name"/>\n- <has_line_matching expression="family\\tEnterobacteriaceae\\t351"/>\n- <has_line_matching expression="genus\\tSalmonella\\t113"/> \n </assert_contents>\n </output>\n </test>\n' |
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| diff -r 9424de64bfa8 -r 822575bf359f test-data/Ecoli_strain_KV7_complete_LT795502.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Ecoli_strain_KV7_complete_LT795502.fasta Fri Jun 05 13:02:15 2020 -0400 |
| b |
| b'@@ -0,0 +1,77768 @@\n+>LT795502.1 Escherichia coli strain KV7 genome assembly, chromosome: I\n+GTGTCACTTTCGCTTTGGCAGCAGTGTCTTGCCCGATTGCAGGATGAGTTACCAGCCACAGAATTCAGTA\n+TGTGGATACGCCCATTGCAGGCGGAACTGAGCGATAACACGCTGGCCCTGTACGCGCCAAACCGTTTTGT\n+CCTCGATTGGGTACGGGACAAGTACCTTAATAATATCAATGGACTGCTAACCAGTTTCTGCGGAGCGGAT\n+GCCCCACAGCTACGTTTTGAAGTCGGCACCAAACCGGTGACGCAAACGCCACAAGCGGCAGTGACGAGCA\n+ACGTCGCGGCCCCTGCACAGGTGGCGCAAACGCAGCCGCAACGTGCTGCGCCTTCTACGCGCTCAGGTTG\n+GGATAACGTCCCGGCCCCGGCAGAACCGACCTATCGTTCTAACGTAAACGTCAAACACACGTTTGATAAC\n+TTCGTTGAAGGTAAATCTAACCAACTGGCGCGCGCGGCGGCTCGCCAGGTGGCGGATAACCCTGGCGGTG\n+CCTATAACCCGTTGTTCCTTTATGGCGGCACGGGTCTGGGTAAAACTCACCTGCTGCATGCGGTGGGTAA\n+CGGCATTATGGCGCGCAAGCCGAATGCCAAAGTGGTTTATATGCACTCCGAGCGCTTTGTTCAGGACATG\n+GTTAAAGCCCTGCAAAACAACGCGATCGAAGAGTTTAAACGCTACTACCGTTCCGTAGATGCACTGCTGA\n+TCGACGATATTCAGTTTTTTGCTAATAAAGAACGATCTCAGGAAGAGTTTTTCCACACCTTCAACGCCCT\n+GCTGGAAGGTAATCAACAGATCATTCTCACCTCGGATCGCTATCCGAAAGAGATCAACGGCGTTGAGGAT\n+CGTTTGAAATCCCGCTTCGGTTGGGGACTGACTGTGGCGATCGAACCGCCAGAGCTGGAAACCCGTGTGG\n+CGATCCTGATGAAAAAGGCCGACGAAAACGACATTCGTTTGCCGGGCGAAGTGGCGTTCTTTATCGCCAA\n+GCGTCTACGATCTAACGTACGTGAGCTGGAAGGGGCGCTGAACCGCGTCATTGCCAATGCCAACTTTACC\n+GGACGGGCGATCACCATCGACTTCGTGCGTGAGGCGCTGCGCGACTTGCTGGCATTGCAGGAAAAACTGG\n+TCACCATCGACAATATTCAGAAGACGGTGGCGGAGTACTACAAGATCAAAGTCGCGGATCTCCTTTCCAA\n+GCGTCGATCCCGCTCGGTGGCGCGTCCGCGCCAGATGGCGATGGCGCTGGCGAAAGAGCTGACTAACCAC\n+AGTCTGCCGGAGATTGGCGATGCGTTTGGTGGCCGTGACCACACGACGGTGCTTCATGCCTGCCGTAAGA\n+TCGAGCAGTTGCGTGAAGAGAGCCACGATATCAAAGAAGATTTTTCAAATTTAATCAGAACATTGTCATC\n+GTAAACCTATGAAATTTACCGTAGAACGTGAGCATTTATTAAAACCGCTACAACAGGTGAGCGGTCCGTT\n+AGGTGGTCGTCCTACGCTACCGATTCTCGGTAATCTGCTGTTACAGGTTGCTGACGGTACGTTATCGCTG\n+ACCGGTACTGATCTCGAGATGGAAATGGTGGCACGTGTTGCGCTGGTTCAGCCACACGAGCCAGGAGCGA\n+CGACCGTTCCGGCGCGCAAATTCTTTGATATCTGCCGTGGTCTGCCTGAAGGCGCGGAAATTGCCGTGCA\n+GCTGGAAGGTGAACGGATGCTGGTACGCTCCGGGCGTAGCCGTTTTTCGCTGTCTACCCTGCCAGCGGCG\n+GATTTCCCGAACCTCGATGACTGGCAGAGTGAAGTCGAATTTACCCTGCCGCAGGCAACGATGAAGCGTC\n+TGATTGAAGCGACCCAGTTTTCTATGGCGCATCAGGACGTTCGCTATTACTTAAATGGTATGCTGTTTGA\n+AACCGAAGGTGAAGAACTGCGCACCGTGGCAACCGACGGCCACCGTCTGGCGGTCTGTTCAATGCCAATT\n+GGTCAATCTTTGCCAAGCCATTCGGTGATCGTACCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCG\n+ACGGCGGCGACAATCCGCTGCGCGTACAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTAT\n+CTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAA\n+CATCTGGAAGCTGGCTGCGATCTGCTCAAGCAGGCGTTTGCTCGCGCGGCGATTCTCTCTAACGAGAAAT\n+TCCGCGGCGTACGTCTTTATGTCAGCGAAAACCAGCTGAAAATCACCGCCAACAACCCGGAACAGGAAGA\n+AGCGGAAGAGATCCTCGACGTTACCTATAGCGGTGCGGAGATGGAAATCGGCTTCAACGTCAGTTATGTG\n+CTGGATGTTCTGAACGCGCTGAAATGCGAAAACGTCCGCATGATGCTGACCGATTCGGTTTCCAGCGTGC\n+AGATTGAAGATGCGGCCAGCCAGAGCGCGGCTTATGTTGTCATGCCAATGAGACTGTAATGTCCCTCACC\n+CGCTTGTTGATCCGCGATTTCCGCAACATTGAAACCGCGGATCTCGCCTTATCTCCCGGCTTTAACTTTC\n+TGGTAGGTGCCAACGGCAGTGGCAAAACCAGCGTGCTGGAAGCCATCTATACGCTCGGCCATGGTCGGGC\n+GTTTCGCAGTTTGCAGATTGGTCGCGTCATTCGCCATGAGCAGGAGGCGTTTGTTCTCCACGGGCGATTA\n+CAGGGCGAAGAGCGCGAGACAGCGATTGGCTTAACCAAAGACAAACAGGGCGACAGCAAAGTCCGCATCG\n+ACGGTACAGACGGGCATAAGGTCGCGGAACTGGCGCACCTGATGCCAATGCAGTTGATAACGCCAGAAGG\n+GTTTACTTTACTCAACGGCGGCCCCAAATACAGAAGAGCATTCCTCGACTGGGGATGCTTTCACAACGAA\n+CCCGGATTTTTCACCGCCTGGAGCAATCTCAAGCGATTGCTCAAGCAGCGCAATGCGGCGCTGCGCCAGG\n+TGACACGTTACGAACAGCTACGCCCGTGGGATAAAGAGCTGATCCCGCTGGCGGAGCAAATCAGCACCTG\n+GCGCGCGGAGTATAGCGCCGGTATCGCGGCCGATATGGCTGATACCTGTAAGCAATTTCTCCCTGAGTTT\n+TCTCTGACTTTCTCTTTCCAGCGCGGCTGGGAGAAAGAGACAGAATATGCTGAGGTGCTGGAACGTAATT\n+TTGAACGCGATCGCCAGCTAACCTACACCGCGCACGGCCCGCACAAAGCGGACTTACGCATTCGCGCCGA\n+CGGTGCGCCGGTGGAAGATACCTTATCGCGTGGGCAGCTTAAGCTGTTGATGTGCGCCTTACGTCTGGCG\n+CAAGGAGAGTTCCTCACCCGTGAAAGCGGGCGGCGGTGTCTCTACCTGATAGATGATTTTGCCTCTGAGC\n+TTGATGATGAGCGTCGCGGGCTGCTTGCCAGCCGCTTAAAAGCGACGCAATCACAGGTCTTTGTCAGCGC\n+GATCAGTGCTGAACACGTTATAGACATGTCGGACGAAAATTCGAAGATGTTTACCGTGGAAAAGGGTAAA\n+ATAACGGATTAACCCAAGTATAAATGAGCGAGAAACGTTGATGTCGAATTCTTATGACTCCTCCAGTATC\n+AAAGTCCTGAAAGGGCTGGATGCGGTGCGTAAGCGCCCGGGTATGTATATCGGCGACACGGATGACGGCA\n+CCGGTCTGCACCACATGGTATTCGAGGTGGTAGATAACGCTATCGACGAAGCGCTCGCGGGTCACTGTAA\n+AGAAATTATCGTCACCAT'..b'AGATTCGCTTAACGGTGCTGGAAATGTTTTGCTTGGAACGGCCTACTCGCGT\n+GGCTACGTCTGATGATTTCTCACCTTTGACAAGCACGGAATAGCCAATATCTGTTGTGATGTGTGCAAAG\n+GAAGCCATTTGCGGCAGCAGCTGTTTCCATTCTGTTTCTGAAATTCTGTTTTTCTGAGCCATCTGTGGCG\n+CCTCCGTAGTTTTGGTTACAGAAAGGATATACTCAGAATAAATAGGGGTCAATACAAGTACGATTTTTAT\n+AAACTTTATTTTATTTGAGGGTGAGGCCCGGTGCGGCAGCAGCGCGGGCCTCGATGGTGCCGCGAAGGTG\n+CTGGCGCCATGCTTGGATTAAAACATGAACCGTGAAGAACTGCGAAACTTGTTTTCGCGGTTCTGAGGGG\n+TTGACCGAGCCGCGAAGCGGCGCTGGTAAGCGATGATATGCACATATCCACAGGCATATTTTTAAAAGGT\n+ATTTTATAGATTTTTTATCTTTTTAAAGTCTTTTAGAGCTATATAACTCATTGATTTAAAATCATAAATA\n+AGTGTTATCTCTGGGAATCCGCCCACCTTGTTATGGGAATTGGCCCACCTATCTATGGGAAACACCCCAC\n+CTTACTATGGGAATTAGCCCACCTTGTTATGGGAATTGGCCCACCTTAGACGAAACTGTAAAAAATGTAT\n+TTACTTGTTTGAACTTTGTGGTAGTGTGGAGAGTAATTTTTAACCCACAAAGGCAAGGCTCATGGATAAG\n+TTGCTGAACAAAAAGATAAAAGTTAAGCAGTCTAACGAGCTTACCGAAGCTGCTTACTACCTCTCGCTAA\n+AAGCAAAGCGCGTTCTCTGGTTATGTCTTATGCAGACGTATTTCACAGCTTCAGTAAGCGAAGATGATGA\n+TGAGATGGCTGTACTCGGTGACTCTACTTTCAAAGTAAAGGTGGCTGACTATCAGCAAATTTTTCAGGTA\n+AGCCGTAACCAGGCTATCAAGGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGCGGTAATCTTTT\n+ACCCGAAAGAAGGGAGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCGGTACATTTACGGCCTGACGAACCAGTTCACC\n+ACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCACGGACGATCCGCCTTTATGAAAGTCTTGCTC\n+AATTCAAATCTTCAGGCTTATGGGTTACTACTCATGCTTGGTTAAATGACCGTTTCCTTTTGCCGGAATC\n+CCAACAGAAGAACTTGGCAGAGTTGAAACGATCTTTCCTTGATCCTGCTCTCAAGCAGATAAATGAGAAA\n+ACACCTTTACTTGCTAAGTATAGTATTGATGATTCAGGAAAATTTCTGTTCTCAATAATTGATAAGCAAA\n+ATCCCGTCTGACATAAATCAGCACACATGAGCCTGTCATTTGACAAATTTTTGTCATGAAGATGGGCGAA\n+TTTCCACACAGCACCGGCGCCCGGCAAGGTGGGCGGATTCCCACACGGCACCGACGCCCGGCAAGGTGGG\n+CGGATTCCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTTCCACACAGCACCGGCGCCCGGCAAGG\n+TGGGCGGATTCCCACACGGCCCGGCAAGGTGGGCGGATTCCCACACGGCACCGGCGCCCGGCAAGGTGGG\n+CGGATTCCCACACAGGCAAGGTGGGCGGATTCCACACGGCACCGCCCGGCAAGGTGGGCGGATTCCCACA\n+CGGCACCGGCGCCCGGCAAGGTGGGCGGATTTCCACACAGCACCGGCGCCCGGCAAGGTGGGCGGATTCC\n+CACACAGCACCGGCGCCCGGCAAGGTGGGCGGATTCCCACACAGCACCGGCGCCCGGCAAGGTGGGCGGA\n+TTTCCACACAGCACCGGCGCCCGGCAAGGTGGGCGGATTCCCACACGGCACCGGCGCCCGGCAAGGTGGG\n+CGGATTCCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTCCCACACGGCACCGGCGCCCGGCAAGG\n+TGGGCGGATTCCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTCCCACACGGCACCGGCGCCCGGC\n+AAGGTGGGCGGATTTCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTTCCACACGGCACCGGCGCC\n+CGGCAAGGTGGGCGGATTCCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTCCCACACGGCACCGG\n+CGCCCGGCAAGGTGGGCGGATTTCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTCCCACACGGCA\n+CCGGCGCCCGGCAAGGTGGGTGGATTTCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTTCCACAC\n+GGCACCGGCGCCCGGCAAGGTGGGCGGATTTCCACACAGCACCGGCGCCCGGCAAGGTGGGCGGATTTCC\n+ACACGGCACCGGCGGCAAGGTGGGCCCCCACTGGGCGGATTCCCACACGGCACCGGCGCCCGGCAAGGTG\n+GGCGGATTTCCACACGGCACCGGCGCCCGGCAAGGTGGGCGGATTTCCACACAGCACCGGCGCCCGGCAA\n+GGTGGGCGGATTTCCACACAGCACCGGCGCCCGGCAAGGTGGGCGGATTTCCATAACTTTAATTATACCT\n+TTGTGTTATTTGTGGATTGTGCAGCTCAGTGGGGCGCTGGCCGTGACGGTGCGGTGTCCCCCGTAACCGG\n+CCGCGCGGCGGCCGCTAACTCGCAGTACGGCGCCGCGACCCGCAGGCGGGCCGCCGTACCCGCGCGCAGG\n+CGCGCGGCGCCCACTGCGCACCCCCGTGGAGGACGTGCGGCAGCTGCGTGGCGGCGGGCTGGGTTATGGC\n+TTAGCAGGGAGGGGGGTTGGCCTGTTGCTCCGGTCAGTCCCGCAGTTTCCGGCGATTTGCGGCCGGTGTC\n+CGGTGGAGTCCGGCGCGGTCGCCTTCCATGCCCTGACGGGCATATGGCGGCACATCGCATTCGACGAAAC\n+CCAACCTAACCGGAGTCATCAGGCTAGAATGTTATTCATCATTTATTTTCTCTGAATGGTTGCCTTTTGT\n+CGTGTAGCGATAAATAGTCATGCGAGAAACATTGAAGCGCTTCGCAACAGCTCCTACTGTCATTTCAGGA\n+TCAGCAAGCAGAATTTTCATTTGCTTAATATCATCTTCCGAAAGTGACGGTTTTCTTCCCCCTACACGGC\n+CCCTTGCGCGAGCAGCTGCGAGTCCAGATCTCGTTCGTTCAATATTGCGGTTGCGTTCAAAGTTAGAGAA\n+TATAGCCATCAGATGAGTATAGATTTCCCCGATAACAGGAGCGCTAGTATCTATTCTGTCTTTGATGGCT\n+ATAAAGGTGATTCCGCGCTTTTTCAGGTCGTCAAGCAACGTAATCACCTGGCTCAATGAACCGCCGAGCC\n+GATCAAGCGCCCAAACAACCAGGGTATCACCTTCGCGCAATGCCTTCAGACAGTTCTCCAGTTCCGGGGC\n+ACCATTTTTGGCGCGTTTAGTGCCGCCGCGTGAGATCTGTTCATGATAGATTTGCTCGCAACCCGCTTTT\n+GTCAGTTCATCAACCTGATGCGTTACATCCTGAAGATGTGTCGATTTACGCGCATAGCCGATTATCATTT\n+TGCCACCCTATTTTGTTACATCGTTTTTGTTGTATTGATACTGTAACGGGTTTTGTTACAGCCGGAGAGC\n+GTTTTATTGTATAGGCAACTGCTTATAGGGATGTGTCACAGAAACCATCGTTTTTGATACATTAATTTAA\n+CCAATAGGTTGCAGATCAAATCGCCTGTAACAGCCTTTCTGGCTGTTTGTATAT\n+\n' |
| b |
| diff -r 9424de64bfa8 -r 822575bf359f test-data/contig_report.txt --- a/test-data/contig_report.txt Wed Dec 11 19:17:11 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -file_id cluster_id contig_id contig_length circularity_status rep_type rep_type_accession relaxase_type relaxase_type_accession mash_nearest_neighbor mash_neighbor_distance repetitive_dna_id match_type score contig_match_start contig_match_end -plasmid_476.fasta 476 plasmid_476.fasta|SRR3703080_illumina_unicycler.fasta|8|length=91194|depth=3.25x 91194 Incomplete IncI1 000145__HE610900_00001 MOBP NC_019097 CP016520 0.000508006 |