Mercurial > repos > nml > staramr
changeset 10:7573a6c11c4d draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 69b939934ff9f503c7314cdbe6e3cb08e5f84db5"
| author | nml |
|---|---|
| date | Wed, 27 Nov 2019 08:59:23 -0500 |
| parents | 61a3e97aa865 |
| children | 5f43703968cf |
| files | staramr_search.xml test-data/test1-resfinder.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 | 10 files changed, 42 insertions(+), 17 deletions(-) [+] |
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--- a/staramr_search.xml Mon Sep 30 12:45:02 2019 -0400 +++ b/staramr_search.xml Wed Nov 27 08:59:23 2019 -0500 @@ -1,7 +1,7 @@ <tool id="staramr_search" name="staramr" version="@VERSION@"> <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> <macros> - <token name="@VERSION@">0.6.1</token> + <token name="@VERSION@">0.7.0</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> @@ -24,6 +24,12 @@ --nprocs "\${GALAXY_SLOTS:-1}" + --genome-size-lower-bound $advanced.genome_size_lower_bound + --genome-size-upper-bound $advanced.genome_size_upper_bound + --minimum-N50-value $advanced.minimum_N50_value + --minimum-contig-length $advanced.minimum_contig_length + --unacceptable-number-contigs $advanced.unacceptable_number_contigs + --pid-threshold $advanced.pid_threshold --percent-length-overlap-resfinder $advanced.plength_resfinder --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder @@ -77,6 +83,16 @@ min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" /> + <param name="genome_size_lower_bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000" + help="(--genome-size-lower-bound)" /> + <param name="genome_size_upper_bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000" + help="(--genome-size-upper-bound)" /> + <param name="minimum_N50_value" type="integer" label="The minimum N50 value for the quality metrics" value="10000" + help="(--minimum-N50-value)" /> + <param name="minimum_contig_length" type="integer" label="The minimum contig length for the quality metrics" value="300" + help="(--minimum-contig-length)" /> + <param name="unacceptable_number_contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000" + help="(--unacceptable-number-contigs)" /> <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> @@ -169,6 +185,13 @@ <output name="summary" file="test5-summary.tsv" ftype="tabular" /> </test> + <test> + <param name="genomes" value="test-aminoglycoside.fsa" /> + <param name="genome_size_lower_bound" value="1" /> + <param name="genome_size_upper_bound" value="10" /> + + <output name="summary" file="test8-summary.tsv" ftype="tabular"/> + </test> </tests> <help><![CDATA[ staramr
--- a/test-data/test1-resfinder.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test1-resfinder.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Gene Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession -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 +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 ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA
--- a/test-data/test1-summary.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test1-summary.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type -16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T), blaIMP-42, gyrA (A67P) spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid None - - +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]
--- a/test-data/test2-resfinder.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test2-resfinder.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Gene Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession -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 +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 ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA
--- a/test-data/test2-summary.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test2-summary.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type -16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None - - +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]
--- a/test-data/test3-summary.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test3-summary.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type -16S-rc_gyrA-rc_beta-lactam.fsa None Sensitive None - - +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]
--- a/test-data/test4-summary.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test4-summary.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type -16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa None Sensitive None - - +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]
--- a/test-data/test5-summary.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test5-summary.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type -test-aminoglycoside.fsa None Sensitive None - - +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]
--- a/test-data/test6-summary.tsv Mon Sep 30 12:45:02 2019 -0400 +++ b/test-data/test6-summary.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type -test-aminoglycoside.fsa aac(6')-Iaa gentamicin None - - +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 gentamicin 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]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8-summary.tsv Wed Nov 27 08:59:23 2019 -0500 @@ -0,0 +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]