Mercurial > repos > nml > staramr

comparison staramr_search.xml @ 11:5f43703968cf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 65ffe1cd11ac6108adf483d3e83856a5466df79c"
author nml
date Wed, 18 Dec 2019 16:14:07 -0500
parents 7573a6c11c4d
children aeaa20b96ef2
comparison
equal deleted inserted replaced
10:7573a6c11c4d 11:5f43703968cf
1 <tool id="staramr_search" name="staramr" version="@VERSION@"> 1 <tool id="staramr_search" name="staramr" version="@VERSION@">
2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> 2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.7.0</token> 4 <token name="@VERSION@">0.7.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">staramr</requirement> 7 <requirement type="package" version="@VERSION@">staramr</requirement>
8 </requirements> 8 </requirements>
9 <version_command>staramr --version</version_command> 9 <version_command>staramr --version</version_command>
247 summary.tsv 247 summary.tsv
248 ``````````` 248 ```````````
249 249
250 A summary of all detected AMR genes/mutations in each genome, one genome per line. 250 A summary of all detected AMR genes/mutations in each genome, one genome per line.
251 251
252 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ 252 | 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 |
253 | Isolate ID | Genotype | Predicted Phenotype | Plasmid | 253 |------------|----------------|-----------------------------------------------------------|-----------------------------------------------------------------------------------------------------------|-------------------------------------|-----------|---------------|---------------|-----------|---------------------------------------------------|-------------------------|
254 +============+===========================================================+===========================================================================================================+=====================================+ 254 | SRR1952908 | Passed | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4796082 | 225419 | 59 | |
255 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | 255 | SRR1952926 | Passed | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11 | 4794071 | 225380 | 50 | |
256 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ 256
257 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 |
258 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
259 257
260 detailed_summary.tsv 258 detailed_summary.tsv
261 ```````````````````` 259 ````````````````````
262 260
263 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line. 261 A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.
372 The command-line, database versions, and other settings used to run `staramr`. 370 The command-line, database versions, and other settings used to run `staramr`.
373 371
374 :: 372 ::
375 373
376 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta 374 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
377 version = 0.6.1 375 version = 0.7.1
378 start_time = 2019-04-25 16:01:32 376 start_time = 2019-04-25 16:01:32
379 end_time = 2019-04-25 16:01:34 377 end_time = 2019-04-25 16:01:34
380 total_minutes = 0.04 378 total_minutes = 0.04
381 resfinder_db_dir = staramr/databases/data/dist/resfinder 379 resfinder_db_dir = staramr/databases/data/dist/resfinder
382 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git 380 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git