comparison staramr_search.xml @ 15:be818ae858e4 draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e92a931da272a26f3a16e7b1d31c432890a6fdb3

14:4b9a8031ab74

<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0">
    <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
    <macros>
        <token name="@VERSION@">0.7.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">staramr</requirement>
    </requirements>
    <version_command>staramr --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re

            #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier))
            ln -s '$genome' $_named_genome &&
            #set $named_genomes = $named_genomes + ' ' + $_named_genome
        #end for

        #set $excel_proper_extension = '"results.xlsx"'
        ln -s "$excel" $excel_proper_extension &&

        staramr search

        --nprocs "\${GALAXY_SLOTS:-1}"

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

        --output-summary $summary
        --output-detailed-summary $detailed_summary
        --output-resfinder $resfinder
        --output-plasmidfinder $plasmidfinder
        #if str($use_pointfinder) != 'disabled'
            --output-pointfinder $pointfinder
        #end if
        --output-settings $settings
        --output-excel $excel_proper_extension
        --output-mlst $mlst

        --output-hits-dir staramr_hits

        #if str($use_pointfinder) != 'disabled'
            --pointfinder-organism '${use_pointfinder}'
        #end if

        $named_genomes
    ]]></command>
    <inputs>
        <param type="data" name="genomes" format="fasta" multiple="true"/>
        <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="salmonella">Salmonella</option>
            <option value="campylobacter">Campylobacter</option>
        </param>
        <section name="advanced" title="Advanced options" expanded="false">
            <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
                   min="0" max="100" help="(--pid-threshold)" />
            <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
                   min="0" max="100" help="(--percent-length-overlap-resfinder)" />

            <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
                   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>
                    <option value="custom">Provide a custom list of AMR genes to exclude</option>

        <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 ${on_string}: resfinder.tsv" />
        <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
        <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
            <filter>use_pointfinder != "disabled"</filter>
        </data>
        <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
        <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
        <collection name="blast_hits" type="list" label="${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" />
            <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" />
                <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
            </output_collection>
        </test>
        <test>
            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />

            <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" />
            </output_collection>
        </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" />
        </test>
        <test>
            <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
            <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" />

            <output name="summary" file="test5-summary.tsv" ftype="tabular" />
        </test>
        <test>
            <param name="genomes" value="test-aminoglycoside.fsa" />
            <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" />
            <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" />
            <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"/>
        </test>

.. _staramr: https://github.com/phac-nml/staramr
.. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
.. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
.. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
.. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
    ]]></help>
    <citations>
        <citation type="bibtex">
            @misc{githubstaramr,
              author = {Petkau, Aaron},
              year = {2018},
              title = {staramr},
              publisher = {GitHub},
              journal = {GitHub repository},
              url = {https://github.com/phac-nml/staramr},
       }</citation>
    </citations>
</tool>

15:be818ae858e4

<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>
    </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>
    </requirements>
    <version_command>staramr --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re

            #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier))
            ln -s '$genome' $_named_genome &&
            #set $named_genomes = $named_genomes + ' ' + $_named_genome
        #end for

        #set $excel_proper_extension = 'results.xlsx'
        ln -s '$excel' $excel_proper_extension &&

        staramr search

        --nprocs "\${GALAXY_SLOTS:-1}"

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

        --output-summary '$summary'
        --output-detailed-summary '$detailed_summary'
        --output-resfinder '$resfinder'
        --output-plasmidfinder '$plasmidfinder'
        --output-settings '$settings'
        --output-excel '$excel_proper_extension'
        --output-mlst '$mlst'

        --output-hits-dir staramr_hits

        #if str($pointfinder_db.use_pointfinder) != 'disabled'
            --output-pointfinder '$pointfinder'
            #if str($pointfinder_db.use_pointfinder) == 'custom'
                --pointfinder-organism '${pointfinder_db.pointfinder_custom}'
            #else
                --pointfinder-organism '${pointfinder_db.use_pointfinder}'
            #end if
        #end if

        $named_genomes
    ]]></command>
    <inputs>
        <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="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="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>
                    <option value="klebsiella">klebsiella</option>
                    <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option>
                    <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option>
                    <option value="plasmodium_falciparum">plasmodium_falciparum</option>
                    <option value="staphylococcus_aureus">staphylococcus_aureus</option>
                </param>
            </when>
        </conditional>
        <section name="advanced" title="Advanced options" expanded="false">
            <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
                   min="0" max="100" help="(--pid-threshold)" />
            <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
                   min="0" max="100" help="(--percent-length-overlap-resfinder)" />

            <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
                   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="aactinomycetemcomitans">aactinomycetemcomitans</option>
                <option value="abaumannii">abaumannii</option>
                <option value="abaumannii_2">abaumannii_2</option>
                <option value="achromobacter">achromobacter</option>
                <option value="aeromonas">aeromonas</option>
                <option value="aphagocytophilum">aphagocytophilum</option>
                <option value="arcobacter">arcobacter</option>
                <option value="bbacilliformis">bbacilliformis</option>
                <option value="bcc">bcc</option>
                <option value="bcereus">bcereus</option>
                <option value="bfragilis">bfragilis</option>
                <option value="bhenselae">bhenselae</option>
                <option value="blicheniformis_14">blicheniformis_14</option>
                <option value="bordetella_3">bordetella_3</option>
                <option value="borrelia">borrelia</option>
                <option value="bpseudomallei">bpseudomallei</option>
                <option value="brachyspira">brachyspira</option>
                <option value="brachyspira_2">brachyspira_2</option>
                <option value="brachyspira_3">brachyspira_3</option>
                <option value="brachyspira_4">brachyspira_4</option>
                <option value="brachyspira_5">brachyspira_5</option>
                <option value="brucella">brucella</option>
                <option value="bsubtilis">bsubtilis</option>
                <option value="bwashoensis">bwashoensis</option>
                <option value="campylobacter">campylobacter</option>
                <option value="campylobacter_nonjejuni">campylobacter_nonjejuni</option>
                <option value="campylobacter_nonjejuni_2">campylobacter_nonjejuni_2</option>
                <option value="campylobacter_nonjejuni_3">campylobacter_nonjejuni_3</option>
                <option value="campylobacter_nonjejuni_4">campylobacter_nonjejuni_4</option>
                <option value="campylobacter_nonjejuni_5">campylobacter_nonjejuni_5</option>
                <option value="campylobacter_nonjejuni_6">campylobacter_nonjejuni_6</option>
                <option value="campylobacter_nonjejuni_7">campylobacter_nonjejuni_7</option>
                <option value="campylobacter_nonjejuni_8">campylobacter_nonjejuni_8</option>
                <option value="campylobacter_nonjejuni_9">campylobacter_nonjejuni_9</option>
                <option value="cbotulinum">cbotulinum</option>
                <option value="cdifficile">cdifficile</option>
                <option value="cfreundii">cfreundii</option>
                <option value="chlamydiales">chlamydiales</option>
                <option value="cmaltaromaticum">cmaltaromaticum</option>
                <option value="cperfringens">cperfringens</option>
                <option value="cronobacter">cronobacter</option>
                <option value="csepticum">csepticum</option>
                <option value="diphtheria_3">diphtheria_3</option>
                <option value="dnodosus">dnodosus</option>
                <option value="ecloacae">ecloacae</option>
                <option value="ecoli">ecoli</option>
                <option value="ecoli_achtman_4">ecoli_achtman_4</option>
                <option value="edwardsiella">edwardsiella</option>
                <option value="efaecalis">efaecalis</option>
                <option value="efaecium">efaecium</option>
                <option value="fpsychrophilum">fpsychrophilum</option>
                <option value="gallibacterium">gallibacterium</option>
                <option value="geotrichum">geotrichum</option>
                <option value="hcinaedi">hcinaedi</option>
                <option value="helicobacter">helicobacter</option>
                <option value="hinfluenzae">hinfluenzae</option>
                <option value="hparasuis">hparasuis</option>
                <option value="hsuis">hsuis</option>
                <option value="kaerogenes">kaerogenes</option>
                <option value="kingella">kingella</option>
                <option value="klebsiella">klebsiella</option>
                <option value="koxytoca">koxytoca</option>
                <option value="leptospira">leptospira</option>
                <option value="leptospira_2">leptospira_2</option>
                <option value="leptospira_3">leptospira_3</option>
                <option value="liberibacter">liberibacter</option>
                <option value="listeria_2">listeria_2</option>
                <option value="llactis_phage">llactis_phage</option>
                <option value="lsalivarius">lsalivarius</option>
                <option value="mabscessus">mabscessus</option>
                <option value="magalactiae">magalactiae</option>
                <option value="manserisalpingitidis">manserisalpingitidis</option>
                <option value="mbovis_2">mbovis_2</option>
                <option value="mcanis">mcanis</option>
                <option value="mcaseolyticus">mcaseolyticus</option>
                <option value="mcatarrhalis_achtman_6">mcatarrhalis_achtman_6</option>
                <option value="mflocculare">mflocculare</option>
                <option value="mgallisepticum">mgallisepticum</option>
                <option value="mgallisepticum_2">mgallisepticum_2</option>
                <option value="mhaemolytica">mhaemolytica</option>
                <option value="mhominis_3">mhominis_3</option>
                <option value="mhyopneumoniae">mhyopneumoniae</option>
                <option value="mhyorhinis">mhyorhinis</option>
                <option value="miowae">miowae</option>
                <option value="mplutonius">mplutonius</option>
                <option value="mpneumoniae">mpneumoniae</option>
                <option value="msciuri">msciuri</option>
                <option value="msynoviae">msynoviae</option>
                <option value="mycobacteria_2">mycobacteria_2</option>
                <option value="neisseria">neisseria</option>
                <option value="oralstrep">oralstrep</option>
                <option value="orhinotracheale">orhinotracheale</option>
                <option value="otsutsugamushi">otsutsugamushi</option>
                <option value="pacnes_3">pacnes_3</option>
                <option value="paeruginosa">paeruginosa</option>
                <option value="pdamselae">pdamselae</option>
                <option value="pfluorescens">pfluorescens</option>
                <option value="pgingivalis">pgingivalis</option>
                <option value="plarvae">plarvae</option>
                <option value="pmultocida">pmultocida</option>
                <option value="pmultocida_2">pmultocida_2</option>
                <option value="ppentosaceus">ppentosaceus</option>
                <option value="pputida">pputida</option>
                <option value="psalmonis">psalmonis</option>
                <option value="ranatipestifer">ranatipestifer</option>
                <option value="rhodococcus">rhodococcus</option>
                <option value="sagalactiae">sagalactiae</option>
                <option value="saureus">saureus</option>
                <option value="sbsec">sbsec</option>
                <option value="scanis">scanis</option>
                <option value="schromogenes">schromogenes</option>
                <option value="sdysgalactiae">sdysgalactiae</option>
                <option value="senterica_achtman_2">senterica_achtman_2</option>
                <option value="sepidermidis">sepidermidis</option>
                <option value="sgallolyticus">sgallolyticus</option>
                <option value="shaemolyticus">shaemolyticus</option>
                <option value="shewanella">shewanella</option>
                <option value="shominis">shominis</option>
                <option value="sinorhizobium">sinorhizobium</option>
                <option value="smaltophilia">smaltophilia</option>
                <option value="spneumoniae">spneumoniae</option>
                <option value="spseudintermedius">spseudintermedius</option>
                <option value="spyogenes">spyogenes</option>
                <option value="ssuis">ssuis</option>
                <option value="staphlugdunensis">staphlugdunensis</option>
                <option value="sthermophilus">sthermophilus</option>
                <option value="streptomyces">streptomyces</option>
                <option value="streptothermophilus">streptothermophilus</option>
                <option value="suberis">suberis</option>
                <option value="szooepidemicus">szooepidemicus</option>
                <option value="taylorella">taylorella</option>
                <option value="tenacibaculum">tenacibaculum</option>
                <option value="tpallidum">tpallidum</option>
                <option value="ureaplasma">ureaplasma</option>
                <option value="vcholerae">vcholerae</option>
                <option value="vcholerae_2">vcholerae_2</option>
                <option value="vibrio">vibrio</option>
                <option value="vparahaemolyticus">vparahaemolyticus</option>
                <option value="vtapetis">vtapetis</option>
                <option value="vvulnificus">vvulnificus</option>
                <option value="wolbachia">wolbachia</option>
                <option value="xfastidiosa">xfastidiosa</option>
                <option value="ypseudotuberculosis_achtman_3">ypseudotuberculosis_achtman_3</option>
                <option value="yruckeri">yruckeri</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>
                    <option value="custom">Provide a custom list of AMR genes to exclude</option>

        <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 ${on_string}: resfinder.tsv" />
        <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" />
        <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
            <filter>pointfinder_db['use_pointfinder'] != "disabled"</filter>
        </data>
        <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
        <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
        <collection name="blast_hits" type="list" label="${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="custom" />
            <param name="pointfinder_custom" 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"/>
        </test>

.. _staramr: https://github.com/phac-nml/staramr
.. _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/
    ]]></help>
    <citations>
        <citation type="bibtex">
            @Article{microorganisms10020292,
            	AUTHOR = {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.},
            	TITLE = {Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr},
            	JOURNAL = {Microorganisms},
            	VOLUME = {10},
            	YEAR = {2022},
            	NUMBER = {2},
            	ARTICLE-NUMBER = {292},
            	URL = {https://www.mdpi.com/2076-2607/10/2/292},
            	ISSN = {2076-2607},
            	DOI = {10.3390/microorganisms10020292}
            }
        </citation>
    </citations>
</tool>