<tool id="homer_install_promoters_data_manager" name="Homer install promoter DB" tool_type="manage_data" version="@TOOL_VERSION@" profile="22.01">
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">homer</requirement>
        <requirement type="package" version="3.11">python</requirement>
    </requirements>
    <macros>
        <token name="@TOOL_VERSION@">4.11</token>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
        cp -r \$(dirname \$(which findMotifs.pl))/../share/homer ./ &&
        perl ./homer/configureHomer.pl -install ${organism}-p ${organism}-o -keepScript &&
        
        organism_version=\$(cat homer/config.txt | grep "accession and ontology information" | grep $organism | cut -f 2) &&
        promoter_version=\$(cat homer/config.txt | grep promoters | grep $organism | cut -f 2) &&
        
        python '$__tool_directory__/homer_install_promoters.py'
            '${out_file}'
            --organism $organism
            --organism_version \${organism_version}
            --promoter_version \${promoter_version}
            --data_table_name homer_promoters
            --DB_path homer
    ]]></command>
    <inputs>
        <param name="organism" type="select" label="Select a target organism to download" help="Promoter, GO and accession information will be downloaded and the data dir will be stored to reduce the network bandwidth during execution of the tool. Always the newest available version will be downloaded.">
            <option value="arabidopsis">arabidopsis (Arabidopsis thaliana)</option>
            <option value="chicken">chicken (Gallus gallus)</option>
            <option value="fly">fly (Drosophila melanogaster)</option>
            <option value="frog">frog (Xenopus tropicalis)</option>
            <option value="human">human (Homo sapiens)</option>
            <option value="mouse">mouse (Mus musculus)</option>
            <option value="rat">rat (Rattus norvegicus)</option>
            <option value="worm" selected="true">worm (Caenorhabditis elegans)</option>
            <option value="yeast">yeast (Saccharomyces cerevisiae)</option>
            <option value="zebrafish">zebrafish (Danio rerio)</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="organism" value="worm"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="{&quot;data_tables&quot;: {&quot;homer_promoters&quot;: [{&quot;dbkey&quot;: &quot;worm_"/>
                    <has_text text="&quot;organism_version&quot;: &quot;v"/>
                    <has_text text="&quot;promoter_version&quot;: &quot;v"/>
                    <has_text text="&quot;organism&quot;: &quot;worm&quot;"/>
                    <has_text text="&quot;path&quot;: &quot;"/>
                </assert_contents>                
            </output>
        </test>
    </tests>
    <help>
    </help>
</tool>