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Commit message:
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84 |
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modified:
staramr_search.xml test-data/genes_to_exclude.tsv test-data/test1-pointfinder-ecoli.tsv test-data/test1-pointfinder.tsv |
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| diff -r be818ae858e4 -r 4d83eccf5f81 staramr_search.xml --- a/staramr_search.xml Wed Jun 22 14:44:55 2022 +0000 +++ b/staramr_search.xml Mon Nov 07 17:33:35 2022 +0000 |
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| @@ -1,14 +1,14 @@ <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04"> <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> <macros> - <token name="@VERSION@">0.8.0</token> + <token name="@VERSION@">0.9.1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> <!-- The staramr conda package includes the mlst software, but the list of schemes changes depending on the version. I specify the exact version here to make sure the list of schemes provided is consistent --> - <requirement type="package" version="2.22.0">mlst</requirement> + <requirement type="package" version="2.23.0">mlst</requirement> </requirements> <version_command>staramr --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -82,23 +82,27 @@ <param type="data" name="genomes" format="fasta" multiple="true"/> <conditional name="pointfinder_db"> <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database"> - <option value="disabled" selected="true">Disable PointFinder</option> + <option value="disabled" selected="true">Disable PointFinder</option> + <option value="campylobacter">Campylobacter</option> + <option value="enterococcus_faecalis">enterococcus_faecalis</option> + <option value="enterococcus_faecium">enterococcus_faecium</option> + <option value="escherichia_coli">escherichia_coli</option> + <option value="helicobacter_pylori">helicobacter_pylori</option> <option value="salmonella">Salmonella</option> - <option value="campylobacter">Campylobacter</option> <option value="custom">Unvalidated</option> </param> <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism --> <when value="disabled"/> + <when value="campylobacter"/> + <when value="enterococcus_faecalis"/> + <when value="enterococcus_faecium"/> + <when value="escherichia_coli"/> + <when value="helicobacter_pylori"/> <when value="salmonella"/> - <when value="campylobacter"/> <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms --> <when value="custom"> - <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results."> - <option value="enterococcus_faecalis">enterococcus_faecalis</option> - <option value="enterococcus_faecium">enterococcus_faecium</option> - <option value="escherichia_coli" selected="true">escherichia_coli</option> - <option value="helicobacter_pylori">helicobacter_pylori</option> + <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results."> <option value="klebsiella">klebsiella</option> <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option> <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option> @@ -328,8 +332,7 @@ </test> <test> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> - <param name="use_pointfinder" value="custom" /> - <param name="pointfinder_custom" value="escherichia_coli" /> + <param name="use_pointfinder" value="escherichia_coli" /> <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" /> <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" /> @@ -395,7 +398,7 @@ staramr ======= -staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes. +staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by their respective webservices_) and compiles a summary report of detected antimicrobial resistance genes. Usage ----- @@ -608,7 +611,7 @@ .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db -.. _webservice: https://cge.food.dtu.dk/services/ResFinder/ +.. _webservices: http://www.genomicepidemiology.org/services/ ]]></help> <citations> <citation type="bibtex"> |
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| diff -r be818ae858e4 -r 4d83eccf5f81 test-data/genes_to_exclude.tsv --- a/test-data/genes_to_exclude.tsv Wed Jun 22 14:44:55 2022 +0000 +++ b/test-data/genes_to_exclude.tsv Mon Nov 07 17:33:35 2022 +0000 |
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| @@ -1,2 +1,2 @@ -#gene_id +gene_id aac(6')-Iaa_1_NC_003197 |
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| diff -r be818ae858e4 -r 4d83eccf5f81 test-data/test1-pointfinder-ecoli.tsv --- a/test-data/test1-pointfinder-ecoli.tsv Wed Jun 22 14:44:55 2022 +0000 +++ b/test-data/test1-pointfinder-ecoli.tsv Mon Nov 07 17:33:35 2022 +0000 |
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| @@ -1,1 +1,1 @@ -Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End +Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End Pointfinder Position |
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| diff -r be818ae858e4 -r 4d83eccf5f81 test-data/test1-pointfinder.tsv --- a/test-data/test1-pointfinder.tsv Wed Jun 22 14:44:55 2022 +0000 +++ b/test-data/test1-pointfinder.tsv Mon Nov 07 17:33:35 2022 +0000 |
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| @@ -1,3 +1,3 @@ -Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End -16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) spectinomycin nucleotide 1065 C -> T 99.94 100.00 1544/1544 16S_rrsD 1604 61 -16S-rc_gyrA-rc_beta-lactam.fsa gyrA (A67P) ciprofloxacin I/R, nalidixic acid codon 67 GCC -> CCC (A -> P) 99.96 100.00 2637/2637 16S_rrsD 4317 1681 +Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End Pointfinder Position +16S-rc_gyrA-rc_beta-lactam.fsa 16S_rrsD (C1065T) spectinomycin nucleotide 1065 C -> T 99.94 100.00 1544/1544 16S_rrsD 1604 61 C1065T +16S-rc_gyrA-rc_beta-lactam.fsa gyrA (A67P) ciprofloxacin I/R, nalidixic acid codon 67 GCC -> CCC (A -> P) 99.96 100.00 2637/2637 16S_rrsD 4317 1681 A67P |