<tool id="cnvkit_export_jtv" name="CNVkit Export JTV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Convert log2 ratios to Java TreeView's native format</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_segmented_file' ./sample.cnr &&
        cnvkit.py export jtv
            ./sample.cnr
            --output sample.cnv.jtv
    ]]></command>
     <inputs>
        <param name="input_segmented_file" type="data" format="cnr" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
        </inputs>
    <outputs>
        <data name="CNVs_cdt" format="jtv" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.jtv" />
    </outputs>
       <tests>
        <test expect_num_outputs="1">
            <param name="input_segmented_file" ftype="tabular" value="sample.cnr" />
            <output name="CNVs_cdt" file="sample.cnv.jtv" />
        </test>
    </tests>
    <help><![CDATA[ 
        This tool converts CNVkit log2 copy ratio data to Java TreeView's native format (.jtv), 
        enabling easy visualisation and clustering analysis with preserved settings for seamless data exploration.

-----

**Bin-level log2 ratios (.cnr)**

Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.

.. csv-table::
   :header-rows: 0

    "chromosome","Genomic chromosome (e.g., chr1, chrX)"
    "start","Start position of the bin."
    "end","End position of the bin."
    "gene","Gene name(s) overlapping the bin (if applicable)."
    "log2","Normalized log2 ratio (sample coverage / reference coverage)."
    "depth","Average read depth in the bin."
    "weight","Reliability weight of the bin (higher = more reliable)."


    ]]></help>
    <expand macro="citations" />
</tool>