Mercurial > repos > nml > staramr
changeset 17:141afacabcfa draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
| author | nml |
|---|---|
| date | Thu, 31 Aug 2023 15:55:49 +0000 |
| parents | 4d83eccf5f81 |
| children | 3b22de20bd4b |
| files | staramr_search.xml test-data/test1-detailed-summary-ecoli.tsv test-data/test1-detailed-summary.tsv test-data/test1-pointfinder-ecoli.tsv test-data/test1-pointfinder.tsv test-data/test1-resfinder.tsv test-data/test1-summary-ecoli.tsv test-data/test1-summary.tsv test-data/test2-resfinder.tsv test-data/test2-summary.tsv test-data/test3-summary.tsv test-data/test4-summary.tsv test-data/test5-summary.tsv test-data/test6-summary.tsv test-data/test8-summary.tsv |
| diffstat | 15 files changed, 61 insertions(+), 46 deletions(-) [+] |
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--- a/staramr_search.xml Mon Nov 07 17:33:35 2022 +0000 +++ b/staramr_search.xml Thu Aug 31 15:55:49 2023 +0000 @@ -1,7 +1,7 @@ <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04"> <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> <macros> - <token name="@VERSION@">0.9.1</token> + <token name="@VERSION@">0.10.0</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> @@ -53,6 +53,11 @@ --no-exclude-genes #end if + + #if str($advanced.complex_mutations.complex_mutations_condition) == 'custom' + --complex-mutations-file '${advanced.complex_mutations.complex_mutations_file}' + #end if + #if str($advanced.plasmidfinder_type) != 'include_all' --plasmidfinder-database-type '${advanced.plasmidfinder_type}' #end if @@ -292,6 +297,16 @@ <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" /> </when> <when value="none" /> + </conditional> + <conditional name="complex_mutations"> + <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations"> + <option value="default" selected="true">Use default list of complex mutations</option> + <option value="custom">Provide a custom list of complex mutations</option> + </param> + <when value="default" /> + <when value="custom"> + <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" /> + </when> </conditional> <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type"> <option value="include_all" selected="true">Include all available database types</option> @@ -316,7 +331,7 @@ </collection> </outputs> <tests> - <test> + <test expect_num_outputs="9"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <param name="use_pointfinder" value="salmonella" /> @@ -324,13 +339,13 @@ <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> - <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> + <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> <output_collection name="blast_hits" type="list"> <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> </output_collection> </test> - <test> + <test expect_num_outputs="9"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <param name="use_pointfinder" value="escherichia_coli" /> @@ -340,7 +355,7 @@ <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <output name="summary" file="test2-summary.tsv" ftype="tabular" /> @@ -349,44 +364,44 @@ <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> </output_collection> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <section name="advanced"> <param name="mlst_scheme" value="listeria_2" /> </section> <output name="mlst" file="mlst.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <param name="pid_threshold" value="99.8" /> <output name="summary" file="test3-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" /> <param name="pid_threshold" value="99.8" /> <output name="summary" file="test4-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <output name="summary" file="test5-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <param name="exclude_genes_condition" value="none" /> <output name="summary" file="test6-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <param name="exclude_genes_condition" value="custom" /> <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> <output name="summary" file="test5-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <param name="genome_size_lower_bound" value="1" /> <param name="genome_size_upper_bound" value="10" />
--- a/test-data/test1-detailed-summary-ecoli.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test1-detailed-summary-ecoli.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,4 +1,4 @@ -Isolate ID Data Data Type Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession -16S-rc_gyrA-rc_beta-lactam.fsa ST- (-) MLST -16S-rc_gyrA-rc_beta-lactam.fsa None Plasmid -16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 Resistance ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456 +Isolate ID Data Data Type Predicted Phenotype CGE Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession +16S-rc_gyrA-rc_beta-lactam.fsa ST- (-) MLST +16S-rc_gyrA-rc_beta-lactam.fsa None Plasmid +16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 Resistance ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456
--- a/test-data/test1-detailed-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test1-detailed-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,6 +1,6 @@ -Isolate ID Data Data Type Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession -16S-rc_gyrA-rc_beta-lactam.fsa ST- (-) MLST -16S-rc_gyrA-rc_beta-lactam.fsa None Plasmid -16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) Resistance spectinomycin 99.94 100.0 1544/1544 16S_rrsD 1604 61 -16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 Resistance ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456 -16S-rc_gyrA-rc_beta-lactam.fsa gyrA (A67P) Resistance ciprofloxacin I/R, nalidixic acid 99.96 100.0 2637/2637 16S_rrsD 4317 1681 +Isolate ID Data Data Type Predicted Phenotype CGE Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession +16S-rc_gyrA-rc_beta-lactam.fsa ST- (-) MLST +16S-rc_gyrA-rc_beta-lactam.fsa None Plasmid +16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) Resistance spectinomycin Spectinomycin 99.94 100.0 1544/1544 16S_rrsD 1604 61 +16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 Resistance ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456 +16S-rc_gyrA-rc_beta-lactam.fsa gyrA (A67P) Resistance ciprofloxacin I/R, nalidixic acid Nalidixic acid,Ciprofloxacin 99.96 100.0 2637/2637 16S_rrsD 4317 1681
--- a/test-data/test1-pointfinder-ecoli.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test1-pointfinder-ecoli.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,1 +1,1 @@ -Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End Pointfinder Position +Isolate ID Gene Predicted Phenotype CGE Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End Pointfinder Position CGE Notes CGE Required Mutation CGE Mechanism CGE PMID
--- a/test-data/test1-pointfinder.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test1-pointfinder.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,3 +1,3 @@ -Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End Pointfinder Position -16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) spectinomycin nucleotide 1065 C -> T 99.94 100.00 1544/1544 16S_rrsD 1604 61 C1065T -16S-rc_gyrA-rc_beta-lactam.fsa gyrA (A67P) ciprofloxacin I/R, nalidixic acid codon 67 GCC -> CCC (A -> P) 99.96 100.00 2637/2637 16S_rrsD 4317 1681 A67P +Isolate ID Gene Predicted Phenotype CGE Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End Pointfinder Position CGE Notes CGE Required Mutation CGE Mechanism CGE PMID +16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) spectinomycin Spectinomycin nucleotide 1065 C -> T 99.94 100.00 1544/1544 16S_rrsD 1604 61 C1065T Target modification 12402084 +16S-rc_gyrA-rc_beta-lactam.fsa gyrA (A67P) ciprofloxacin I/R, nalidixic acid Nalidixic acid,Ciprofloxacin codon 67 GCC -> CCC (A -> P) 99.96 100.00 2637/2637 16S_rrsD 4317 1681 A67P gyrA_G81C.S.H.D Target modification 7492118
--- a/test-data/test1-resfinder.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test1-resfinder.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Gene Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession Sequence -16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.00 741/741 16S_rrsD 4381 5121 AB753456 ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA +Isolate ID Gene Predicted Phenotype CGE Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession Sequence CGE Notes +16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam 99.73 100.00 741/741 16S_rrsD 4381 5121 AB753456 ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA Subclass B1
--- a/test-data/test1-summary-ecoli.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test1-summary-ecoli.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -16S-rc_gyrA-rc_beta-lactam.fsa Failed blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +16S-rc_gyrA-rc_beta-lactam.fsa Failed blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
--- a/test-data/test1-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test1-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -16S-rc_gyrA-rc_beta-lactam.fsa Failed 16S_rrsD (C1065T), blaIMP-42, gyrA (A67P) spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +16S-rc_gyrA-rc_beta-lactam.fsa Failed 16S_rrsD (C1065T), blaIMP-42, gyrA (A67P) spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid Spectinomycin, Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam, Nalidixic acid, Ciprofloxacin None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
--- a/test-data/test2-resfinder.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test2-resfinder.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Gene Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession Sequence -16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.00 741/741 16S_rrsD 4381 5121 AB753456 ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA +Isolate ID Gene Predicted Phenotype CGE Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession Sequence CGE Notes +16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam 99.73 100.00 741/741 16S_rrsD 4381 5121 AB753456 ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA Subclass B1
--- a/test-data/test2-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test2-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -16S-rc_gyrA-rc_beta-lactam.fsa Failed blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +16S-rc_gyrA-rc_beta-lactam.fsa Failed blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
--- a/test-data/test3-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test3-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -16S-rc_gyrA-rc_beta-lactam.fsa Failed None Sensitive None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +16S-rc_gyrA-rc_beta-lactam.fsa Failed None Susceptible - None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
--- a/test-data/test4-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test4-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa Failed None Sensitive None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa Failed None Susceptible - None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
--- a/test-data/test5-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test5-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -test-aminoglycoside.fsa Failed None Sensitive None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +test-aminoglycoside.fsa Failed None Susceptible - None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
--- a/test-data/test6-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test6-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -test-aminoglycoside.fsa Failed aac(6')-Iaa unknown[aac(6')-Iaa_1_NC_003197] None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +test-aminoglycoside.fsa Failed aac(6')-Iaa unknown[aac(6')-Iaa_1_NC_003197] Amikacin, Tobramycin None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
--- a/test-data/test8-summary.tsv Mon Nov 07 17:33:35 2022 +0000 +++ b/test-data/test8-summary.tsv Thu Aug 31 15:55:49 2023 +0000 @@ -1,2 +1,2 @@ -Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -test-aminoglycoside.fsa Failed None Sensitive None - - 438 438 1 Genome length is not within the acceptable length range [1,10] ; N50 value is not greater than the specified minimum value [10000] +Isolate ID Quality Module Genotype Predicted Phenotype CGE Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +test-aminoglycoside.fsa Failed None Susceptible - None - - 438 438 1 Genome length is not within the acceptable length range [1,10] ; N50 value is not greater than the specified minimum value [10000]