annotate staramr_search.xml @ 14:4b9a8031ab74 draft

"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit bb824050809fecf04d8f17cd4419033c18927f45"

<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_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 $plasmidfinder
        #if str($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="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="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>
                    <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 ${on_string}: pointfinder.tsv">
            <filter>use_pointfinder != "disabled"</filter>
        </data>
        <data format="txt" name="settings" label="${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>
    </tests>
    <help><![CDATA[
staramr
=======

staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.

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
.. _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>