<tool id="abritamr" name="abriTAMR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>AMR gene detection with AMRFinderPlus</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.14</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@PROFILE@">22.05</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">abritamr</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">abritamr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
abritamr run
    --contigs '$input_tsv'
#if $species:
    --species '$species'
#end if
#if $identity:
    --identity '$identity'
#end if
    --jobs \${GALAXY_SLOTS:-4}
]]></command>
    <configfiles>
        <configfile name="input_tsv">
#for $i in $contig:
${i.element_identifier}	${i}
#end for
        </configfile>
    </configfiles>
    <inputs>
        <param name="contig" type="data" format="fasta" multiple="true" label="Input contigs"/>
        <param argument="species" type="select" multiple="false" optional="true" label="Specify species to aquire resistance mechanisms as point mutations">
            <option value="Neisseria">Neisseria</option>
            <option value="Clostridioides_difficile">Clostridioides difficile</option>
            <option value="Acinetobacter_baumannii">Acinetobacter baumannii</option>
            <option value="Campylobacter">Campylobacter</option>
            <option value="Enterococcus_faecalis">Enterococcus faecalis</option>
            <option value="Enterococcus_faecium">Enterococcus faecium</option>
            <option value="Escherichia">Escherichia</option>
            <option value="Klebsiella">Klebsiella</option>
            <option value="Salmonella">Salmonella</option>
            <option value="Staphylococcus_aureus">Staphylococcus aureus</option>
            <option value="Staphylococcus_pseudintermedius">Staphylococcus pseudintermedius</option>
            <option value="Streptococcus_agalactiae">Streptococcus agalactiae</option>
            <option value="Streptococcus_pneumoniae">Streptococcus pneumoniae</option>
            <option value="Streptococcus_pyogenes">Streptococcus pyogenes</option>
        </param>
        <param argument="identity" type="float" optional="true" min="0.0" max="1.0" label="Minimum identity of matches with armfinder" help="The default is unset, uses a curated threshold for the gene if present, otherwise defaults to 0.9."/>
        <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
    </inputs>
    <outputs>
        <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
        <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
        <data name="partials_summary" format="txt" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
        <data name="virulence_summary" format="txt" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
        <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log">
            <filter>log_file</filter>
        </data>
    </outputs>
    <tests>
        <!-- Single sample, with logfile -->
        <test expect_num_outputs="5">
            <param name="contig" value="CP009102.1.fasta" />
            <param name="log_file" value="true" />
            <output name="virulence_summary" ftype="txt">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_text text="sinH"/>
                </assert_contents>
            </output>
        </test>
        <!-- Multiple samples, no logfile -->
        <test expect_num_outputs="4">
            <param name="contig" value="NC_003198.1_1kb.fasta,NC_011750.1_1kb.fasta" />
            <param name="species" value="Salmonella" />
            <param name="identity" value="0.9" />
            <param name="log_file" value="false" />
            <output name="virulence_summary" ftype="txt">
                <assert_contents>
                    <has_n_lines n="3"/>
                    <has_text text="NC_003198.1_1kb.fasta"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
*Taming the AMR beast*

abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia.
    + Acquired resistance mechanims in the form of point mutations (restricted to subset of species)
    + Streamlined output.
    + Presence of virulence factors
    </help>
    <citations>
        <citation type="doi">10.5281/zenodo.7370627</citation>
    </citations>
</tool>