<tool id="lrn_risk" name="PIMA: LRNRisk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>isolate classification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/lrn_risk.py'
--gtdb_file '$gtdb_file'
--virulence_factors_file '$virulence_factors_file'
--amr_determinants_file '$amr_determinants_file'
--blacklist_file '$blacklist_file'
--vf_distribution_file '$vf_distribution_file'
--amr_distribution_file '$amr_distribution_file'
--blacklist_output_file '$blacklist_output_file'
--vfdb_output_file '$vfdb_output_file'
--amr_output_file '$amr_output_file'
]]></command>
    <inputs>
        <param name="gtdb_file" type="data" format="tabular,tsv" label="GTDB-Tk Classify genomes file"/>
        <param name="virulence_factors_file" type="data" format="tabular,tsv" label="File containing virulence factors detected via BLAST"/>
        <param name="amr_determinants_file" type="data" format="tabular,tsv" label="File containing Pima AMR determinants detected via BLAST"/>
        <param name="blacklist_file" type="data" format="tabular,tsv" label="File containing blacklisted high-risk virulence factors"/>
        <param name="vf_distribution_file" type="data" format="tabular,tsv" label="File containing virulence factor distribution"/>
        <param name="amr_distribution_file" type="data" format="tabular,tsv" label="File containing AMR determinant distribution"/>
    </inputs>
    <outputs>
        <data name="blacklist_output_file" format="tsv" label="${tool.name} on ${on_string} (blacklist)"/>
        <data name="vfdb_output_file" format="tsv" label="${tool.name} on ${on_string} (VFDB)"/>
        <data name="amr_output_file" format="tsv" label="${tool.name} on ${on_string} (AMR)"/>
    </outputs>
    <tests>
        <test>
            <param name="gtdb_file" value="gtdb.tsv" ftype="tsv"/>
            <param name="virulence_factors_file" value="virulence_factors.tsv" ftype="tsv"/>
            <param name="amr_determinants_file" value="amr_determinants.tsv" ftype="tsv"/>
            <param name="blacklist_file" value="blacklist.tsv" ftype="tsv"/>
            <param name="vf_distribution_file" value="vf_distribution.tsv" ftype="tsv"/>
            <param name="amr_distribution_file" value="amr_distribution.tsv" ftype="tsv"/>
            <output name="blacklist_output_file" value="blacklist.tsv" ftype="tsv"/>
            <output name="vfdb_output_file" value="vfdb_output.tsv" ftype="tsv"/>
            <output name="amr_output_file" value="amr_output.tsv" ftype="tsv"/>
        </test>
    </tests>
    <help>
**What it does**

Classifies isolates into "high risk" and "unlikely high risk" and provides information about prevalence of a given virulence
gene among all publicly available genome of a given species and prevalence of a given antimicrobial resistance gene among all
publicly available genomes of a given species. 
    </help>
    <expand macro="citations"/>
</tool>