# HG changeset patch # User nml # Date 1596210966 14400 # Node ID 2fd4d4c9c5c2b4b8bbab5eb7117bf1b6c9d13149 # Parent aeaa20b96ef2531b7464443d53a58397d201013b "planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" diff -r aeaa20b96ef2 -r 2fd4d4c9c5c2 staramr_search.xml --- a/staramr_search.xml Sat Apr 04 19:27:12 2020 -0400 +++ b/staramr_search.xml Fri Jul 31 11:56:06 2020 -0400 @@ -1,7 +1,7 @@ - + Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes. - 0.7.1 + 0.7.1 staramr @@ -35,6 +35,10 @@ --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder --percent-length-overlap-pointfinder $advanced.plength_pointfinder + #if str($advanced.mlst_scheme) != 'auto': + --mlst-scheme '${advanced.mlst_scheme}' + #end if + $advanced.report_all_blast $advanced.exclude_negatives $advanced.exclude_resistance_phenotypes @@ -58,6 +62,7 @@ #end if --output-settings $settings --output-excel $excel_proper_extension + --output-mlst $mlst --output-hits-dir staramr_hits @@ -97,6 +102,141 @@ help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -117,7 +257,7 @@ - + @@ -134,7 +274,7 @@ - + @@ -157,6 +297,13 @@ +

+ +

+ + + + @@ -249,10 +396,13 @@ A summary of all detected AMR genes/mutations in each genome, one genome per line. ++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+ | 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 | -|------------|----------------|-----------------------------------------------------------|-----------------------------------------------------------------------------------------------------------|-------------------------------------|-----------|---------------|---------------|-----------|---------------------------------------------------|-------------------------| ++============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+ | 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 | | ++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+ | 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 | | ++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+ detailed_summary.tsv diff -r aeaa20b96ef2 -r 2fd4d4c9c5c2 test-data/mlst.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mlst.tsv Fri Jul 31 11:56:06 2020 -0400 @@ -0,0 +1,2 @@ +Isolate ID Scheme Sequence Type Locus 1 Locus 2 Locus 3 Locus 4 Locus 5 Locus 6 Locus 7 +16S-rc_gyrA-rc_beta-lactam.fsa kpneumoniae - gapA(-) infB(-) mdh(-) pgi(-) phoE(-) rpoB(-) tonB(-)