Mercurial > repos > nml > staramr
changeset 9:61a3e97aa865 draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
| author | nml |
|---|---|
| date | Mon, 30 Sep 2019 12:45:02 -0400 |
| parents | da787fc8b740 |
| children | 7573a6c11c4d |
| files | staramr_search.xml test-data/test1-detailed-summary.tsv test-data/test1-summary.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 |
| diffstat | 8 files changed, 37 insertions(+), 21 deletions(-) [+] |
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--- a/staramr_search.xml Mon Jun 24 15:21:42 2019 -0400 +++ b/staramr_search.xml Mon Sep 30 12:45:02 2019 -0400 @@ -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@">0.5.1</token> + <token name="@VERSION@">0.6.1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> @@ -101,6 +101,7 @@ </section> </inputs> <outputs> + <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" /> <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> @@ -117,7 +118,7 @@ <tests> <test> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> - <param name="use_pointfinder" value="salmonella" /> + <param name="use_pointfinder" value="salmonella" /> <output name="summary" file="test1-summary.tsv" ftype="tabular" /> <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> @@ -204,7 +205,21 @@ Output ------ -There are 5 different output files produced by `staramr` as well as a collection of additional files. +There are 6 different output files produced by `staramr` as well as a collection of additional files. + +mlst.tsv +```````````````````` + +A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line. + ++------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ +| Isolate ID | Scheme | Sequence Type | Locus 1 | Locus 2 | Locus 3 | Locus 4 | Locus 5 | Locus 6 | Locus 7 | ++============+==============+===================================+============+============+============+============+============+============+============+ +| SRR1952908 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | ++------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+ +| SRR1952926 | senterica | 11 | aroC(5) | dnaN(2) | hemD(3) | hisD(7) | purE(6) | sucA(6) | thrA(11) | ++------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+ + summary.tsv ``````````` @@ -336,7 +351,7 @@ :: command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta - version = 0.5.1 + version = 0.6.1 start_time = 2019-04-25 16:01:32 end_time = 2019-04-25 16:01:34 total_minutes = 0.04
--- a/test-data/test1-detailed-summary.tsv Mon Jun 24 15:21:42 2019 -0400 +++ b/test-data/test1-detailed-summary.tsv Mon Sep 30 12:45:02 2019 -0400 @@ -1,5 +1,6 @@ -Isolate ID Gene/Plasmid Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession Data Type -16S-rc_gyrA-rc_beta-lactam.fsa None Plasmid -16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) spectinomycin 99.94 100.0 1544/1544 16S_rrsD 1604 61 Resistance -16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456 Resistance -16S-rc_gyrA-rc_beta-lactam.fsa gyrA (A67P) ciprofloxacin I/R, nalidixic acid 99.96 100.0 2637/2637 16S_rrsD 4317 1681 Resistance +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
--- a/test-data/test1-summary.tsv Mon Jun 24 15:21:42 2019 -0400 +++ b/test-data/test1-summary.tsv Mon Sep 30 12:45:02 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid -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 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 - -
--- a/test-data/test2-summary.tsv Mon Jun 24 15:21:42 2019 -0400 +++ b/test-data/test2-summary.tsv Mon Sep 30 12:45:02 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid -16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None +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 - -
--- a/test-data/test3-summary.tsv Mon Jun 24 15:21:42 2019 -0400 +++ b/test-data/test3-summary.tsv Mon Sep 30 12:45:02 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid -16S-rc_gyrA-rc_beta-lactam.fsa None Sensitive None +Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type +16S-rc_gyrA-rc_beta-lactam.fsa None Sensitive None - -
--- a/test-data/test4-summary.tsv Mon Jun 24 15:21:42 2019 -0400 +++ b/test-data/test4-summary.tsv Mon Sep 30 12:45:02 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid -16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa None Sensitive None +Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type +16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa None Sensitive None - -
--- a/test-data/test5-summary.tsv Mon Jun 24 15:21:42 2019 -0400 +++ b/test-data/test5-summary.tsv Mon Sep 30 12:45:02 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid -test-aminoglycoside.fsa None Sensitive None +Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type +test-aminoglycoside.fsa None Sensitive None - -
--- a/test-data/test6-summary.tsv Mon Jun 24 15:21:42 2019 -0400 +++ b/test-data/test6-summary.tsv Mon Sep 30 12:45:02 2019 -0400 @@ -1,2 +1,2 @@ -Isolate ID Genotype Predicted Phenotype Plasmid -test-aminoglycoside.fsa aac(6')-Iaa gentamicin None +Isolate ID Genotype Predicted Phenotype Plasmid Scheme Sequence Type +test-aminoglycoside.fsa aac(6')-Iaa gentamicin None - -