<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 '$input_segmented_file' ./sample.cnr &&
        cnvkit.py export nexus-basic
            ./sample.cnr
            --output sample.cnv.tsv
    ]]></command>
     <inputs>
        <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
        </inputs>
    <outputs>
        <data name="CNVs_NexusBasic" format="tabular" label="${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="tabular" 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.
    ]]></help>
    <expand macro="citations" />
</tool>