comparison staramr_search.xml @ 17:141afacabcfa draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303

16:4d83eccf5f81

<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>
    </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

        #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
            --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
        #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
            --no-exclude-genes
        #end if

        #if str($advanced.plasmidfinder_type) != 'include_all'
            --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
        #end if

                <when value="default" />
                <when value="custom">
                    <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>
            <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
                <option value="include_all" selected="true">Include all available database types</option>
                <option value="gram_positive">Gram Positive</option>
                <option value="enterobacteriaceae">Enterobacteriaceae</option>

        <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
            <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            <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" />
            <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_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>
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            <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" />
            <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
            <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
            <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" />
        </test>
        <test>
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />

            <output name="summary" file="test2-summary.tsv" ftype="tabular" />
            <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
            <output_collection name="blast_hits" type="list">
                <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>
            <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>
            <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>
            <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>
            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />

            <output name="summary" file="test5-summary.tsv" ftype="tabular" />
        </test>
        <test>
            <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>
            <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>
            <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" />

            <output name="summary" file="test8-summary.tsv" ftype="tabular"/>

17:141afacabcfa

<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@">0.10.0</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

        #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
            --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
        #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
            --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

                <when value="default" />
                <when value="custom">
                    <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>
                <option value="gram_positive">Gram Positive</option>
                <option value="enterobacteriaceae">Enterobacteriaceae</option>

        <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
            <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="9">
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            <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" />
            <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_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 expect_num_outputs="9">
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
            <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" />
            <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
            <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
            <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" />
        </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" />
            <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
            <output_collection name="blast_hits" type="list">
                <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 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 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 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 expect_num_outputs="8">
            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />

            <output name="summary" file="test5-summary.tsv" ftype="tabular" />
        </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 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 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" />

            <output name="summary" file="test8-summary.tsv" ftype="tabular"/>