<tool id="calculate_density" name="Calculate Density" version="1.0.0">
    <description>Calculate coverage density from BED/GFF files</description>
    <requirements>
        <requirement type="package" version="1.7.3">r-optparse</requirement>
        <requirement type="package" version="1.54.0">bioconductor-rtracklayer</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="calculate_density.R"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/calculate_density.R'
        --bed '$input_bed'
        --window '$window_size'
        --output '$output_bigwig'
        --format '$input_bed.ext'
        #if $merge:
          --merge
        #end if
    ]]></command>
    <inputs>
        <param type="data" format="bed,gff" name="input_bed" label="Input BED/GFF file" help="BED or GFF file containing genomic regions" />
        <param type="integer" name="window_size" label="Window size" value="1000000" min="1" help="Size of the window for density calculation" />
        <param type="boolean" name="merge" label="Merge overlapping regions" truevalue="true" falsevalue="false" checked="true" help="Merge overlapping regions before calculating density" />
    </inputs>
    <outputs>
        <data format="bigwig" name="output_bigwig" label="${tool.name} on ${on_string}: BigWig output"/>
    </outputs>
    <help><![CDATA[
        This tool calculates the coverage density from a provided BED or GFF file over specified window sizes and outputs the results in BigWig format.
    ]]></help>

</tool>