annotate staramr_search.xml @ 16:4d83eccf5f81 draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84

<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
             the list of schemes provided is consistent -->
	<requirement type="package" version="2.23.0">mlst</requirement>
    </requirements>
    <version_command>staramr --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re

        #set $named_genomes = ''
        #for $genome in $genomes
            #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}"

        --genome-size-lower-bound $advanced.genome_size_lower_bound
        --genome-size-upper-bound $advanced.genome_size_upper_bound
        --minimum-N50-value $advanced.minimum_N50_value
        --minimum-contig-length $advanced.minimum_contig_length
        --unacceptable-number-contigs $advanced.unacceptable_number_contigs

        --pid-threshold $advanced.pid_threshold
        --percent-length-overlap-resfinder $advanced.plength_resfinder
        --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder
        --percent-length-overlap-pointfinder $advanced.plength_pointfinder

        #if str($advanced.mlst_scheme) != 'auto':
            --mlst-scheme '${advanced.mlst_scheme}'
        #end if

        $advanced.report_all_blast
        $advanced.exclude_negatives
        $advanced.exclude_resistance_phenotypes

        #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

        --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="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="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"/>

	    <!-- 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="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="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
                   min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
            <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0"
                   min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" />
            <param name="genome_size_lower_bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000"
                   help="(--genome-size-lower-bound)" />
            <param name="genome_size_upper_bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000"
                   help="(--genome-size-upper-bound)" />
            <param name="minimum_N50_value" type="integer" label="The minimum N50 value for the quality metrics" value="10000"
                   help="(--minimum-N50-value)" />
            <param name="minimum_contig_length" type="integer" label="The minimum contig length for the quality metrics" value="300"
                   help="(--minimum-contig-length)" />
            <param name="unacceptable_number_contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000"
                   help="(--unacceptable-number-contigs)" />
            <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>
                    <option value="none">Do not exclude any AMR genes</option>
                </param>
                <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>
            </param>
        </section>
    </inputs>
    <outputs>
    <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
        <data format="tabular" name="summary" label="${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="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>
    </tests>
    <help><![CDATA[
staramr
=======

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
-----

1. Select your genome contigs (in FASTA format).
2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* and *campylobacter* is supported).
3. Run the tool.

Input
-----

Genomes
```````

staramr_ takes as input one or more assembled genomes (in FASTA format) to search for AMR genes.

Exclude genes file
``````````````````

Setting **Provide a custom list of AMR genes to exclude** in the **Advanced options** allows you to pass a file containing a list of genes to exclude from the results. The file must start with a line **#gene_id** and the gene names must correspond to the sequence IDs in the ResFinder/PointFinder databases.  For example:

::

    #gene_id
    aac(6')-Iaa_1_NC_003197
    ColpVC_1__JX133088

Output
------

There are 6 different output files produced by `staramr` as well as a collection of additional files.

mlst.tsv
````````````````````

A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.

+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
| Isolate ID | Scheme       | Sequence Type                     | Locus 1    | Locus 2    | Locus 3    | Locus 4    | Locus 5    | Locus 6    | Locus 7    |
+============+==============+===================================+============+============+============+============+============+============+============+
| SRR1952908 | senterica    | 11                                | aroC(5)    | dnaN(2)    | hemD(3)    | hisD(7)    | purE(6)    | sucA(6)    | thrA(11)   |
+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+
| SRR1952926 | senterica    | 11                                | aroC(5)    | dnaN(2)    | hemD(3)    | hisD(7)    | purE(6)    | sucA(6)    | thrA(11)   |
+------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+


summary.tsv
```````````

A summary of all detected AMR genes/mutations in each genome, one genome per line.

+------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
| 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 |
+============+================+===========================================================+===========================================================================================================+=====================================+===========+===============+===============+===========+===================================================+=========================+
| SRR1952908 | Passed         | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11            | 4796082       | 225419    | 59                                                |                         |
+------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+
| SRR1952926 | Passed         | blaTEM-57, gyrA (S83Y), tet(A)                            | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline                                               | ColpVC, IncFIB(S), IncFII(S), IncI1 | senterica | 11            | 4794071       | 225380    | 50                                                |                         |
+------------+----------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+-----------+---------------+---------------+-----------+---------------------------------------------------+-------------------------+


detailed_summary.tsv
````````````````````

A detailed summary of all detected AMR genes/mutations/plasmids in each genome/type, one gene/type per line.

+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| Isolate ID | Gene/Plasmid | Predicted Phenotype               | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start  | End    | Accession | Data Type  |
+============+==============+===================================+===========+==========+=========================+=============+========+========+===========+============+
| SRR1952908 | ColpVC       |                                   | 98.96     | 100      | 193/193                 | contig00038 | 1618   | 1426   | JX133088  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | IncFIB(S)    |                                   | 98.91     | 100      | 643/643                 | contig00024 | 10302  | 9660   | FN432031  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | IncFII(S)    |                                   | 100       | 100      | 262/262                 | contig00024 | 54294  | 54555  | CP000858  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | IncI1        |                                   | 100       | 100      | 142/142                 | contig00020 | 3907   | 3766   | AP005147  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | aadA1        | streptomycin                      | 100       | 100      | 792/792                 | contig00030 | 5355   | 4564   | JQ414041  | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | aadA2        | streptomycin                      | 100       | 100      | 780/780                 | contig00030 | 7748   | 6969   | X68227    | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | blaTEM-57    | ampicillin                        | 99.88     | 100      | 861/861                 | contig00032 | 6247   | 5387   | FJ405211  | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | cmlA1        | chloramphenicol                   | 99.92     | 100      | 1260/1260               | contig00030 | 6707   | 5448   | M64556    | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid | 99.96     | 100      | 2637/2637               | contig00008 | 22801  | 20165  |           | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | sul3         | sulfisoxazole                     | 100       | 100      | 792/792                 | contig00030 | 2091   | 2882   | AJ459418  | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952908 | tet(A)       | tetracycline                      | 99.92     | 97.8     | 1247/1275               | contig00032 | 1476   | 2722   | AF534183  | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952926 | ColpVC       |                                   | 98.96     | 100      | 193/193                 | contig00037 | 657    | 849    | JX133088  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952926 | IncFIB(S)    |                                   | 98.91     | 100      | 643/643                 | contig00021 | 10302  | 9660   | FN432031  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952926 | IncFII(S)    |                                   | 100       | 100      | 262/262                 | contig00021 | 54294  | 54555  | CP000858  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952926 | IncI1        |                                   | 100       | 100      | 142/142                 | contig00017 | 3907   | 3766   | AP005147  | Plasmid    |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952926 | blaTEM-57    | ampicillin                        | 99.88     | 100      | 861/861                 | contig00027 | 6176   | 5316   | FJ405211  | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952926 | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid | 99.96     | 100      | 2637/2637               | contig00011 | 157768 | 160404 |           | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+
| SRR1952926 | tet(A)       | tetracycline                      | 99.92     | 97.8     | 1247/1275               | contig00027 | 1405   | 2651   | AF534183  | Resistance |
+------------+--------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+


resfinder.tsv
`````````````

A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.

+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| Isolate ID | Gene       | Predicted Phenotype  | %Identity  | %Overlap  | HSP Length/Total Length  | Contig       | Start  | End   | Accession |
+============+============+======================+============+===========+==========================+==============+========+=======+===========+
| SRR1952908 | sul3       | sulfisoxazole        | 100.00     | 100.00    | 792/792                  | contig00030  | 2091   | 2882  | AJ459418  |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| SRR1952908 | tet(A)     | tetracycline         | 99.92      | 100.00    | 1200/1200                | contig00032  | 1551   | 2750  | AJ517790  |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| SRR1952908 | cmlA1      | chloramphenicol      | 99.92      | 100.00    | 1260/1260                | contig00030  | 6707   | 5448  | M64556    |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| SRR1952908 | aadA1      | streptomycin         | 100.00     | 100.00    | 792/792                  | contig00030  | 5355   | 4564  | JQ414041  |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| SRR1952908 | aadA2      | streptomycin         | 99.75      | 100.00    | 792/792                  | contig00030  | 7760   | 6969  | JQ364967  |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| SRR1952908 | blaTEM-57  | ampicillin           | 99.88      | 100.00    | 861/861                  | contig00032  | 6247   | 5387  | FJ405211  |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| SRR1952926 | tet(A)     | tetracycline         | 99.92      | 100.00    | 1200/1200                | contig00027  | 1480   | 2679  | AJ517790  |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
| SRR1952926 | blaTEM-57  | ampicillin           | 99.88      | 100.00    | 861/861                  | contig00027  | 6176   | 5316  | FJ405211  |
+------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+

plasmidfinder.tsv
`````````````````

A tabular file of each AMR plasmid type and additional BLAST information from the **PlasmidFinder** database, one plasmid type per line.

+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| Isolate ID | Plasmid   | %Identity | %Overlap | HSP Length/Total Length | Contig      | Start | End   | Accession |
+============+===========+===========+==========+=========================+=============+=======+=======+===========+
| SRR1952908 | ColpVC    | 98.96     | 100      | 193/193                 | contig00038 | 1618  | 1426  | JX133088  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| SRR1952908 | IncFIB(S) | 98.91     | 100      | 643/643                 | contig00024 | 10302 | 9660  | FN432031  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| SRR1952908 | IncFII(S) | 100       | 100      | 262/262                 | contig00024 | 54294 | 54555 | CP000858  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| SRR1952908 | IncI1     | 100       | 100      | 142/142                 | contig00020 | 3907  | 3766  | AP005147  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| SRR1952926 | ColpVC    | 98.96     | 100      | 193/193                 | contig00037 | 657   | 849   | JX133088  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| SRR1952926 | IncFIB(S) | 98.91     | 100      | 643/643                 | contig00021 | 10302 | 9660  | FN432031  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| SRR1952926 | IncFII(S) | 100       | 100      | 262/262                 | contig00021 | 54294 | 54555 | CP000858  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+
| SRR1952926 | IncI1     | 100       | 100      | 142/142                 | contig00017 | 3907  | 3766  | AP005147  |
+------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+

pointfinder.tsv
```````````````

A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.

+-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
| Isolate ID  | Gene         | Predicted Phenotype                | Type   | Position  | Mutation             | %Identity  | %Overlap  | HSP Length/Total Length  | Contig       | Start   | End    |
+=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
| SRR1952908  | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid  | codon  | 83        | TCC -> TAC (S -> Y)  | 99.96      | 100.00    | 2637/2637                | contig00008  | 22801   | 20165  |
+-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
| SRR1952926  | gyrA (S83Y)  | ciprofloxacin I/R, nalidixic acid  | codon  | 83        | TCC -> TAC (S -> Y)  | 99.96      | 100.00    | 2637/2637                | contig00011  | 157768  | 160404 |
+-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+

settings.txt
````````````

The command-line, database versions, and other settings used to run `staramr`.

::

    command_line                  = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
    version                       = 0.7.1
    start_time                    = 2019-04-25 16:01:32
    end_time                      = 2019-04-25 16:01:34
    total_minutes                 = 0.04
    resfinder_db_dir              = staramr/databases/data/dist/resfinder
    resfinder_db_url              = https://bitbucket.org/genomicepidemiology/resfinder_db.git
    resfinder_db_commit           = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
    resfinder_db_date             = Mon, 16 Jul 2018 16:58
    pointfinder_db_dir            = staramr/databases/data/dist/pointfinder
    pointfinder_db_url            = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
    pointfinder_db_commit         = 8706a6363bb29e47e0e398c53043b037c24b99a7
    pointfinder_db_date           = Wed, 04 Jul 2018 14:27
    plasmidfinder_db_dir          = staramr/databases/data/dist/plasmidfinder
    plasmidfinder_db_url          = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
    plasmidfinder_db_commit       = 81919954cbedaff39056610ab584ab4c06011ed8
    plasmidfinder_db_date         = Tue, 20 Nov 2018 08:51
    pointfinder_gene_drug_version = 050218
    resfinder_gene_drug_version   = 050218.1

results.xlsx
````````````

An Excel spreadsheet containing the previous 5 files as separate worksheets.

BLAST Hits
``````````

The dataset collection  **hits** stores fasta files of the specific blast hits.

Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.

.. _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
.. _webservices: http://www.genomicepidemiology.org/services/
    ]]></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>