<tool id="argnorm" name="argNorm" version="@VERSION@+galaxy0" profile="22.05">
    <description>a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)</description>
    <macros>
        <token name="@VERSION@">0.6.0</token>
    </macros>
    <xrefs>
       <xref type="bio.tools">argnorm</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@VERSION@">argnorm</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    argnorm
        '$tool'
        --db '$db'
        -i '$input' 
        -o '$output'
        $hamronized
    ]]></command>
    <inputs>
        <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" />
        <param type="select" name="tool" label="The tool you used to do ARG annotation" help="[tool]" >
            <option value="deeparg" selected="true">DeepARG</option>
            <option value="argsoap">ARGs_OAP</option>
            <option value="abricate">ABRicate</option>
            <option value="resfinder">ResFinder</option>
            <option value="amrfinderplus">AMRFinderPlus</option>
            <option value="groot">Groot</option>
        </param>
        <param type="select" argument="--db" label="The database you used to do ARG annotation">
            <option value="sarg" selected="true">SARG</option>
            <option value="ncbi">NCBI</option>
            <option value="resfinder">ResFinder</option>
            <option value="deeparg" selected="true">DeepARG</option>
            <option value="amrfinderplus">AMRFinderPlus</option>
            <option value="megares">MEGARes</option>
            <option value="argannot">ARG-ANNOT</option>
            <option value="groot-resfinder">Groot ResFinder database </option>
            <option value="groot-argannot">Groot ARG-ANNOT database </option>
            <option value="groot-card">Groot CARD database </option>
            <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option>
            <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option>
        </param> 
        <param name="hamronized" type="boolean" label="If the input is hamronized" truevalue="--hamronized" falsevalue="" optional="true" help="Use this if the input is hamronized (processed using the hAMRonization tool)" />
    </inputs>
    <outputs>
        <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" />
    </outputs>
    <tests>
        <!-- Test 1 : input : tsv, output : tsv, tool : groot -->
        <test>
            <param name="input" value="resfinder_PSM7J199_R2.report"/>
            <param name="tool" value="groot"/>
            <param name="db" value="groot-resfinder"/>
            <output name="output" file="groot-resfinder-results.tsv"/>
        </test>
        <!-- Test 2 : input : txt, output : tsv, tool : argsoap -->
        <test>
            <param name="input" value="blastout.filtered.txt"/>
            <param name="tool" value="argsoap"/>
            <param name="db" value="sarg"/>
            <output name="output" file="blastout.filtered.argnorm.tsv"/>
        </test>
        <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize : true -->
        <test>
            <param name="input" value="deeparg_hamronize.tsv"/>
            <param name="tool" value="deeparg"/>
            <param name="db" value="deeparg"/>
            <param name="hamronized" value="true"/>
            <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/>
        </test>
    </tests>
    <help><![CDATA[

argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.

argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.

    ]]></help>
    <citations>
        <citation type="doi">https://github.com/BigDataBiology/argNorm</citation>
    </citations>
</tool>