| Previous changeset 14:4b9a8031ab74 (2021-03-05) Next changeset 16:4d83eccf5f81 (2022-11-07) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3 |
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modified:
staramr_search.xml test-data/mlst.tsv test-data/test6-summary.tsv |
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added:
test-data/test1-detailed-summary-ecoli.tsv test-data/test1-pointfinder-ecoli.tsv test-data/test1-summary-ecoli.tsv |
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| diff -r 4b9a8031ab74 -r be818ae858e4 staramr_search.xml --- a/staramr_search.xml Fri Mar 05 16:04:58 2021 +0000 +++ b/staramr_search.xml Wed Jun 22 14:44:55 2022 +0000 |
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| b'@@ -1,10 +1,14 @@\n-<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0">\n+<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">\n <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>\n <macros>\n- <token name="@VERSION@">0.7.2</token>\n+ <token name="@VERSION@">0.8.0</token>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">staramr</requirement>\n+\t<!-- The staramr conda package includes the mlst software, but the list of schemes \n+\t changes depending on the version. I specify the exact version here to make sure\n+ the list of schemes provided is consistent -->\n+\t<requirement type="package" version="2.22.0">mlst</requirement>\n </requirements>\n <version_command>staramr --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n@@ -17,8 +21,8 @@\n #set $named_genomes = $named_genomes + \' \' + $_named_genome\n #end for\n \n- #set $excel_proper_extension = \'"results.xlsx"\'\n- ln -s "$excel" $excel_proper_extension &&\n+ #set $excel_proper_extension = \'results.xlsx\'\n+ ln -s \'$excel\' $excel_proper_extension &&\n \n staramr search\n \n@@ -53,32 +57,56 @@\n --plasmidfinder-database-type \'${advanced.plasmidfinder_type}\'\n #end if\n \n- --output-summary $summary\n- --output-detailed-summary $detailed_summary\n- --output-resfinder $resfinder\n- --output-plasmidfinder $plasmidfinder\n- #if str($use_pointfinder) != \'disabled\'\n- --output-pointfinder $pointfinder\n- #end if\n- --output-settings $settings\n- --output-excel $excel_proper_extension\n- --output-mlst $mlst\n+ --output-summary \'$summary\'\n+ --output-detailed-summary \'$detailed_summary\'\n+ --output-resfinder \'$resfinder\'\n+ --output-plasmidfinder \'$plasmidfinder\'\n+ --output-settings \'$settings\'\n+ --output-excel \'$excel_proper_extension\'\n+ --output-mlst \'$mlst\'\n \n --output-hits-dir staramr_hits\n \n- #if str($use_pointfinder) != \'disabled\'\n- --pointfinder-organism \'${use_pointfinder}\'\n+ #if str($pointfinder_db.use_pointfinder) != \'disabled\'\n+ --output-pointfinder \'$pointfinder\'\n+ #if str($pointfinder_db.use_pointfinder) == \'custom\'\n+ --pointfinder-organism \'${pointfinder_db.pointfinder_custom}\'\n+ #else\n+ --pointfinder-organism \'${pointfinder_db.use_pointfinder}\'\n+ #end if\n #end if\n \n $named_genomes\n ]]></command>\n <inputs>\n <param type="data" name="genomes" format="fasta" multiple="true"/>\n- <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">\n- <option value="disabled" selected="true">Disable PointFinder</option>\n- <option value="salmonella">Salmonella</option>\n- <option value="campylobacter">Campylobacter</option>\n- </param>\n+ <conditional name="pointfinder_db">\n+ <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">\n+ <option value="disabled" selected="true">Disable PointFinder</option>\n+ <option value="salmonella">Salmonella</option>\n+ <option value="campylobacter">Campylobacter</option>\n+ <option value="custom">Unvalidated</option>\n+ </param>\n+\t <!-- These three values don\'t have any additional parameters as they are used as-is to control the PointFinder organism -->\n+\t <when value="disabled"/>\n+\t <when value="salmonella"/>\n+\t <when value="campylobacter"/>\n+\n+\t <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organis'..b'" value="listeria_2" />\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="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />\n <param name="pid_threshold" value="99.8" />\n \n <output name="summary" file="test3-summary.tsv" ftype="tabular" />\n </test>\n <test>\n- <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />\n+ <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" />\n <param name="pid_threshold" value="99.8" />\n \n <output name="summary" file="test4-summary.tsv" ftype="tabular" />\n </test>\n <test>\n- <param name="genomes" value="test-aminoglycoside.fsa" />\n+ <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />\n \n <output name="summary" file="test5-summary.tsv" ftype="tabular" />\n </test>\n <test>\n- <param name="genomes" value="test-aminoglycoside.fsa" />\n+ <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />\n <param name="exclude_genes_condition" value="none" />\n \n <output name="summary" file="test6-summary.tsv" ftype="tabular" />\n </test>\n <test>\n- <param name="genomes" value="test-aminoglycoside.fsa" />\n+ <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />\n <param name="exclude_genes_condition" value="custom" />\n <param name="exclude_genes_file" value="genes_to_exclude.tsv" />\n \n <output name="summary" file="test5-summary.tsv" ftype="tabular" />\n </test>\n <test>\n- <param name="genomes" value="test-aminoglycoside.fsa" />\n+ <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />\n <param name="genome_size_lower_bound" value="1" />\n <param name="genome_size_upper_bound" value="10" />\n \n@@ -557,17 +608,22 @@\n .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db\n .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db\n .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db\n-.. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/\n+.. _webservice: https://cge.food.dtu.dk/services/ResFinder/\n ]]></help>\n <citations>\n <citation type="bibtex">\n- @misc{githubstaramr,\n- author = {Petkau, Aaron},\n- year = {2018},\n- title = {staramr},\n- publisher = {GitHub},\n- journal = {GitHub repository},\n- url = {https://github.com/phac-nml/staramr},\n- }</citation>\n+ @Article{microorganisms10020292,\n+ \tAUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.},\n+ \tTITLE = {Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr},\n+ \tJOURNAL = {Microorganisms},\n+ \tVOLUME = {10},\n+ \tYEAR = {2022},\n+ \tNUMBER = {2},\n+ \tARTICLE-NUMBER = {292},\n+ \tURL = {https://www.mdpi.com/2076-2607/10/2/292},\n+ \tISSN = {2076-2607},\n+ \tDOI = {10.3390/microorganisms10020292}\n+ }\n+ </citation>\n </citations>\n </tool>\n' |
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| diff -r 4b9a8031ab74 -r be818ae858e4 test-data/mlst.tsv --- a/test-data/mlst.tsv Fri Mar 05 16:04:58 2021 +0000 +++ b/test-data/mlst.tsv Wed Jun 22 14:44:55 2022 +0000 |
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| @@ -1,2 +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(-) +16S-rc_gyrA-rc_beta-lactam.fsa listeria_2 - abcZ(-) bglA(-) cat(-) dapE(-) dat(-) ldh(-) lhkA(-) |
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| diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test1-detailed-summary-ecoli.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-detailed-summary-ecoli.tsv Wed Jun 22 14:44:55 2022 +0000 |
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| @@ -0,0 +1,4 @@ +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 blaIMP-42 Resistance ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456 |
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| diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test1-pointfinder-ecoli.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-pointfinder-ecoli.tsv Wed Jun 22 14:44:55 2022 +0000 |
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| @@ -0,0 +1,1 @@ +Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End |
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| diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test1-summary-ecoli.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-summary-ecoli.tsv Wed Jun 22 14:44:55 2022 +0000 |
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| @@ -0,0 +1,2 @@ +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 +16S-rc_gyrA-rc_beta-lactam.fsa Failed blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] |
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| diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test6-summary.tsv --- a/test-data/test6-summary.tsv Fri Mar 05 16:04:58 2021 +0000 +++ b/test-data/test6-summary.tsv Wed Jun 22 14:44:55 2022 +0000 |
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| @@ -1,2 +1,2 @@ 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 -test-aminoglycoside.fsa Failed aac(6')-Iaa gentamicin None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +test-aminoglycoside.fsa Failed aac(6')-Iaa unknown[aac(6')-Iaa_1_NC_003197] None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] |