| Previous changeset 12:aeaa20b96ef2 (2020-04-04) Next changeset 14:4b9a8031ab74 (2021-03-05) |
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Commit message:
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e" |
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modified:
staramr_search.xml |
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added:
test-data/mlst.tsv |
| b |
| 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 |
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| b'@@ -1,7 +1,7 @@\n-<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1">\n+<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy2">\n <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>\n <macros>\n-\t <token name="@VERSION@">0.7.1</token>\n+ <token name="@VERSION@">0.7.1</token>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">staramr</requirement>\n@@ -35,6 +35,10 @@\n --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder\n --percent-length-overlap-pointfinder $advanced.plength_pointfinder\n \n+ #if str($advanced.mlst_scheme) != \'auto\':\n+ --mlst-scheme \'${advanced.mlst_scheme}\'\n+ #end if\n+\n $advanced.report_all_blast\n $advanced.exclude_negatives\n $advanced.exclude_resistance_phenotypes\n@@ -58,6 +62,7 @@\n #end if\n --output-settings $settings\n --output-excel $excel_proper_extension\n+ --output-mlst $mlst\n \n --output-hits-dir staramr_hits\n \n@@ -97,6 +102,141 @@\n help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />\n <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />\n <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />\n+ <param name="mlst_scheme" type="select" label="MLST Scheme">\n+ <option value="auto" selected="true">Automatic</option>\n+ <option value="abaumannii">Acinetobacter baumannii</option>\n+ <option value="abaumannii_2">Acinetobacter baumannii</option>\n+ <option value="achromobacter">Achromobacter </option>\n+ <option value="aeromonas">Aeromonas </option>\n+ <option value="afumigatus">Aspergillus afumigatus</option>\n+ <option value="aphagocytophilum">Anaplasma aphagocytophilum</option>\n+ <option value="arcobacter">Arcobacter </option>\n+ <option value="bburgdorferi">Borrelia burgdorferi</option>\n+ <option value="bcc">Burkholderia cepacia</option>\n+ <option value="bcereus">Bacillus cereus</option>\n+ <option value="bhampsonii">Brachyspira hampsonii</option>\n+ <option value="bhenselae">Bartonella henselae</option>\n+ <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option>\n+ <option value="bifidobacterium">Bifidobacterium bifidobacterium</option>\n+ <option value="bintermedia">Brachyspira intermedia</option>\n+ <option value="blicheniformis">Bacillus licheniformis</option>\n+ <option value="bordetella">Bordetella pertussis</option>\n+ <option value="borrelia">Borrelia </option>\n+ <option value="bpilosicoli">Brachyspira pilosicoli</option>\n+ <option value="bpseudomallei">Burkholderia pseudomallei</option>\n+ <option value="brachyspira">Brachyspira </option>\n+ <option value="bsubtilis">Bacillus subtilis</option>\n+ <option value="calbicans">Candida albicans</option>\n+ <option value="campylobacter">Campylobacter coli</option>\n+ <option value="campylobacter">Campylobacter jejuni</option>\n+ <option value="cbotulinum">Clostridium botulinum</option>\n+ <option value="cconcisus">Campylobacter concisus</option>\n+ <option value="cdifficile">Clostridium difficile</option>\n+ <option value="cdifficile">Peptoclostridium difficile</option>\n+ <option value="cdifficile_2">Clostridium difficile</option>\n+ <'..b' <param name="use_pointfinder" value="salmonella" /> \n+ <param name="use_pointfinder" value="salmonella" />\n \n <output name="summary" file="test1-summary.tsv" ftype="tabular" />\n <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />\n@@ -157,6 +297,13 @@\n </test>\n <test>\n <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />\n+ <section name="advanced">\n+ <param name="mlst_scheme" value="kpneumoniae" />\n+ </section>\n+ <output name="mlst" file="mlst.tsv" ftype="tabular" />\n+ </test>\n+ <test>\n+ <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />\n <param name="pid_threshold" value="99.8" />\n \n <output name="summary" file="test3-summary.tsv" ftype="tabular" />\n@@ -249,10 +396,13 @@\n \n A summary of all detected AMR genes/mutations in each genome, one genome per line.\n \n++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+\n | 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 |\n-|------------|----------------|-----------------------------------------------------------|-----------------------------------------------------------------------------------------------------------|-------------------------------------|-----------|---------------|---------------|-----------|---------------------------------------------------|-------------------------|\n++============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+\n | 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 | |\n++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+\n | 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 | |\n++------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+\n \n \n detailed_summary.tsv\n' |
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| 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 |
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| @@ -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(-) |