<tool id="cnvkit_export_nexus_basic" name="CNVkit Export Nexus Basics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Convert bin-level log2 ratios to Nexus Copy Number "basic" 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 '$input_segmented_file' ./sample.cnr &&
        cnvkit.py export nexus-basic
            ./sample.cnr
            --output sample.cnv.tsv
    ]]></command>
     <inputs>
        <param name="input_segmented_file" type="data" format="cnr,cns" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
        </inputs>
    <outputs>
        <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" />
    </outputs>
       <tests>
        <test expect_num_outputs="1">
            <param name="input_segmented_file" ftype="cnr" value="sample.cnr" />
            <output name="CNVs_NexusBasic" file="sample.cnv.tsv" />
        </test>
    </tests>
    <help><![CDATA[ 

This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format, 
enabling efficient visualisation and analysis of genomic alterations in Nexus software. 
This conversion facilitates downstream interpretation and integration with other genomic data.
    
-----

**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>