<tool id="cnvkit_export_cdt" name="CNVkit Export CDT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Convert log2 ratios to Clustered Data Table (CDT)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_segmented_file' ./sample.cnr &&
        cnvkit.py export cdt
            ./sample.cnr
            --output sample.cnv.cdt
    ]]></command>
     <inputs>
        <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
        </inputs>
    <outputs>
        <data name="CNVs_cdt" format="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" />
    </outputs>
       <tests>
        <test expect_num_outputs="1">
            <param name="input_segmented_file" ftype="tabular" value="sample.cnr" />
            <output name="CNVs_cdt" file="sample.cnv.cdt" />
        </test>
    </tests>
    <help><![CDATA[ 
        This tool converts CNVkit log2 copy ratio data to the CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering. 
        The conversion enables efficient exploration and interpretation of genomic copy number variations.
    ]]></help>
    <expand macro="citations" />
</tool>