Mercurial > repos > nml > staramr
diff staramr_search.xml @ 17:141afacabcfa draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
author | nml |
---|---|
date | Thu, 31 Aug 2023 15:55:49 +0000 |
parents | 4d83eccf5f81 |
children | 3b22de20bd4b |
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--- a/staramr_search.xml Mon Nov 07 17:33:35 2022 +0000 +++ b/staramr_search.xml Thu Aug 31 15:55:49 2023 +0000 @@ -1,7 +1,7 @@ <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@">0.9.1</token> + <token name="@VERSION@">0.10.0</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> @@ -53,6 +53,11 @@ --no-exclude-genes #end if + + #if str($advanced.complex_mutations.complex_mutations_condition) == 'custom' + --complex-mutations-file '${advanced.complex_mutations.complex_mutations_file}' + #end if + #if str($advanced.plasmidfinder_type) != 'include_all' --plasmidfinder-database-type '${advanced.plasmidfinder_type}' #end if @@ -292,6 +297,16 @@ <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" /> </when> <when value="none" /> + </conditional> + <conditional name="complex_mutations"> + <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations"> + <option value="default" selected="true">Use default list of complex mutations</option> + <option value="custom">Provide a custom list of complex mutations</option> + </param> + <when value="default" /> + <when value="custom"> + <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" /> + </when> </conditional> <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type"> <option value="include_all" selected="true">Include all available database types</option> @@ -316,7 +331,7 @@ </collection> </outputs> <tests> - <test> + <test expect_num_outputs="9"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <param name="use_pointfinder" value="salmonella" /> @@ -324,13 +339,13 @@ <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> - <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> + <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> <output_collection name="blast_hits" type="list"> <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> </output_collection> </test> - <test> + <test expect_num_outputs="9"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <param name="use_pointfinder" value="escherichia_coli" /> @@ -340,7 +355,7 @@ <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <output name="summary" file="test2-summary.tsv" ftype="tabular" /> @@ -349,44 +364,44 @@ <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> </output_collection> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <section name="advanced"> <param name="mlst_scheme" value="listeria_2" /> </section> <output name="mlst" file="mlst.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> <param name="pid_threshold" value="99.8" /> <output name="summary" file="test3-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" /> <param name="pid_threshold" value="99.8" /> <output name="summary" file="test4-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <output name="summary" file="test5-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <param name="exclude_genes_condition" value="none" /> <output name="summary" file="test6-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <param name="exclude_genes_condition" value="custom" /> <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> <output name="summary" file="test5-summary.tsv" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="8"> <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> <param name="genome_size_lower_bound" value="1" /> <param name="genome_size_upper_bound" value="10" />