Mercurial > repos > nml > staramr
changeset 13:2fd4d4c9c5c2 draft
"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit f328deb1fae95c3418e86bc1f1a2b2034b2f7c3e"
| author | nml |
|---|---|
| date | Fri, 31 Jul 2020 11:56:06 -0400 |
| parents | aeaa20b96ef2 |
| children | 4b9a8031ab74 |
| files | staramr_search.xml test-data/mlst.tsv |
| diffstat | 2 files changed, 157 insertions(+), 5 deletions(-) [+] |
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--- 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 @@ -<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1"> +<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy2"> <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> <macros> - <token name="@VERSION@">0.7.1</token> + <token name="@VERSION@">0.7.1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> @@ -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)" /> <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" /> + <param name="mlst_scheme" type="select" label="MLST Scheme"> + <option value="auto" selected="true">Automatic</option> + <option value="abaumannii">Acinetobacter baumannii</option> + <option value="abaumannii_2">Acinetobacter baumannii</option> + <option value="achromobacter">Achromobacter </option> + <option value="aeromonas">Aeromonas </option> + <option value="afumigatus">Aspergillus afumigatus</option> + <option value="aphagocytophilum">Anaplasma aphagocytophilum</option> + <option value="arcobacter">Arcobacter </option> + <option value="bburgdorferi">Borrelia burgdorferi</option> + <option value="bcc">Burkholderia cepacia</option> + <option value="bcereus">Bacillus cereus</option> + <option value="bhampsonii">Brachyspira hampsonii</option> + <option value="bhenselae">Bartonella henselae</option> + <option value="bhyodysenteriae">Brachyspira hyodysenteriae</option> + <option value="bifidobacterium">Bifidobacterium bifidobacterium</option> + <option value="bintermedia">Brachyspira intermedia</option> + <option value="blicheniformis">Bacillus licheniformis</option> + <option value="bordetella">Bordetella pertussis</option> + <option value="borrelia">Borrelia </option> + <option value="bpilosicoli">Brachyspira pilosicoli</option> + <option value="bpseudomallei">Burkholderia pseudomallei</option> + <option value="brachyspira">Brachyspira </option> + <option value="bsubtilis">Bacillus subtilis</option> + <option value="calbicans">Candida albicans</option> + <option value="campylobacter">Campylobacter coli</option> + <option value="campylobacter">Campylobacter jejuni</option> + <option value="cbotulinum">Clostridium botulinum</option> + <option value="cconcisus">Campylobacter concisus</option> + <option value="cdifficile">Clostridium difficile</option> + <option value="cdifficile">Peptoclostridium difficile</option> + <option value="cdifficile_2">Clostridium difficile</option> + <option value="cdiphtheriae">Corynebacterium diphtheriae</option> + <option value="cfetus">Campylobacter fetus</option> + <option value="cfreundii">Citrobacter freundii</option> + <option value="cglabrata">Candida glabrata</option> + <option value="chelveticus">Campylobacter helveticus</option> + <option value="chlamydiales">Chlamydia </option> + <option value="chyointestinalis">Campylobacter hyointestinalis</option> + <option value="cinsulaenigrae">Campylobacter insulaenigrae</option> + <option value="ckrusei">Candida krusei</option> + <option value="clanienae">Campylobacter lanienae</option> + <option value="clari">Campylobacter lari</option> + <option value="cmaltaromaticum">Carnobacterium maltaromaticum</option> + <option value="cneoformans">Cryptococcus neoformans</option> + <option value="cronobacter">Cronobacter </option> + <option value="csepticum">Clostridium septicum</option> + <option value="csinensis">Clonorchis sinensis</option> + <option value="csputorum">Campylobacter sputorum</option> + <option value="ctropicalis">Candida tropicalis</option> + <option value="cupsaliensis">Campylobacter upsaliensis</option> + <option value="ecloacae">Enterobacter cloacae</option> + <option value="ecoli">Escherichia </option> + <option value="ecoli">Shigella </option> + <option value="ecoli_2">Escherichia </option> + <option value="edwardsiella">Edwardsiella tarda</option> + <option value="efaecalis">Enterococcus faecalis</option> + <option value="efaecium">Enterococcus faecium</option> + <option value="fpsychrophilum">Flavobacterium psychrophilum</option> + <option value="haemophilus">Haemophilus </option> + <option value="hcinaedi">Helicobacter cinaedi</option> + <option value="hinfluenzae">Haemophilus influenzae</option> + <option value="hparasuis">Haemophilus parasuis</option> + <option value="hpylori">Helicobacter pylori</option> + <option value="hsuis">Haematopinus suis</option> + <option value="kkingae">Kingella kingae</option> + <option value="koxytoca">Klebsiella oxytoca</option> + <option value="kpneumoniae">Klebsiella pneumoniae</option> + <option value="kseptempunctata">Kudoa septempunctata</option> + <option value="lcasei">Lactobacillus casei</option> + <option value="legionella">Legionella </option> + <option value="leptospira">Leptospira </option> + <option value="leptospira_2">Leptospira </option> + <option value="leptospira_3">Leptospira </option> + <option value="lmonocytogenes">Listeria monocytogenes</option> + <option value="lsalivarius">Lactobacillus salivarius</option> + <option value="mabscessus">Mycobacterium abscessus</option> + <option value="magalactiae">Mycoplasma agalactiae</option> + <option value="mbovis">Mycoplasma bovis</option> + <option value="mcatarrhalis">Moraxells catarrhalis</option> + <option value="mhaemolytica">Mannheimia haemolytica</option> + <option value="mhyorhinis">Mycoplasma hyorhinis</option> + <option value="mmassiliense">Mycobacterium massiliense</option> + <option value="mplutonius">Melissococcus plutonius</option> + <option value="neisseria">Neisseria </option> + <option value="orhinotracheale">Ornithobacterium rhinotracheale</option> + <option value="otsutsugamushi">Orientia tsutsugamushi</option> + <option value="pacnes">Propionibacterium acnes</option> + <option value="paeruginosa">Pseudomonas aeruginosa</option> + <option value="pagglomerans">Pantoea agglomerans</option> + <option value="pfluorescens">Pseudomonas fluorescens</option> + <option value="pfreudenreichii">Propionibacterium freudenreichii</option> + <option value="pgingivalis">Porphyromonas gingivalis</option> + <option value="plarvae">Paenibacillus larvae</option> + <option value="pmultocida_multihost">Pasteurella multocida</option> + <option value="pmultocida_rirdc">Pasteurella multocida</option> + <option value="ppentosaceus">Pediococcus pentosaceus</option> + <option value="pshigelloides">Plesiomonas shigelloides</option> + <option value="ranatipestifer">Riemerella anatipestifer</option> + <option value="sagalactiae">Streptococcus agalactiae</option> + <option value="saureus">Staphylococcus aureus</option> + <option value="scanis">Streptococcus canis</option> + <option value="sdysgalactiae">Streptococcus dysgalactiae</option> + <option value="senterica">Salmonella enterica</option> + <option value="sepidermidis">Staphylococcus epidermidis</option> + <option value="sgallolyticus">Streptococcus gallolyticus</option> + <option value="shaemolyticus">Staphylococcus haemolyticus</option> + <option value="shominis">Stapylococcus hominis</option> + <option value="sinorhizobium">Sinorhizobium </option> + <option value="slugdunensis">Staphylococcus lugdunensis</option> + <option value="smaltophilia">Stenotrophomonas maltophilia</option> + <option value="soralis">Streptococcus oralis</option> + <option value="spneumoniae">Streptococcus pneumoniae</option> + <option value="spseudintermedius">Staphylococcus pseudintermedius</option> + <option value="spyogenes">Streptococcus pyogenes</option> + <option value="ssuis">Streptococcus suis</option> + <option value="sthermophilus">Streptococcus thermophilus</option> + <option value="sthermophilus_2">Streptococcus thermophilus</option> + <option value="streptomyces">Streptomyces </option> + <option value="suberis">Streptococcus uberis</option> + <option value="szooepidemicus">Streptococcus equi</option> + <option value="taylorella">Taylorella </option> + <option value="tenacibaculum">Tenacibaculum </option> + <option value="tvaginalis">Trichomonas vaginalis</option> + <option value="vcholerae">Vibrio cholerae</option> + <option value="vibrio">Vibrio </option> + <option value="vparahaemolyticus">Vibrio parahaemolyticus</option> + <option value="vtapetis">Vibrio tapetis</option> + <option value="vvulnificus">Vibrio vulnificus</option> + <option value="wolbachia">Wolbachia </option> + <option value="xfastidiosa">Xylella fastidiosa</option> + <option value="yersinia">Yersinia </option> + <option value="ypseudotuberculosis">Yersinia pseudotuberculosis</option> + <option value="yruckeri">Yersinia ruckeri</option> + </param> <conditional name="exclude_genes"> <param name="exclude_genes_condition" type="select" label="Exclude certain AMR genes from the results"> <option value="default" selected="true">Exclude default list of AMR genes</option> @@ -117,7 +257,7 @@ </section> </inputs> <outputs> - <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" /> + <data format="tabular" name="mlst" label="${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" /> @@ -134,7 +274,7 @@ <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" /> @@ -157,6 +297,13 @@ </test> <test> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> + <section name="advanced"> + <param name="mlst_scheme" value="kpneumoniae" /> + </section> + <output name="mlst" file="mlst.tsv" ftype="tabular" /> + </test> + <test> + <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> <param name="pid_threshold" value="99.8" /> <output name="summary" file="test3-summary.tsv" ftype="tabular" /> @@ -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
--- /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(-)