<tool id="cnvkit_export_seg" name="CNVkit Export SEG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Convert segments to Segment (SEG) 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.cns &&
        cnvkit.py export seg
            ./sample.cns
            $advanced_settings.enumerate_chroms  
            --output sample.cnv.seg
    ]]></command>
     <inputs>
        <param name="input_segmented_file" type="data" format="cns" label="Segmented copy ratio data file (cns file)" help="" />
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" />
        </section>  
        </inputs>
    <outputs>
        <data name="CNVs_SEG" format="seg" label="${tool.name} on ${on_string}: CNVs SEG file" from_work_dir="sample.cnv.seg" />
    </outputs>
       <tests>
        <test expect_num_outputs="1">
            <param name="input_segmented_file" ftype="cns" value="sample.cns" />
            <output name="CNVs_SEG" file="sample.cnv.seg" />
        </test>
    </tests>
    <help><![CDATA[
        Export the segmented copy number data (from a .cns file) to the standard SEG format. 
    
-----

**Segmented log2 ratios (.cns)**

Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.

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

    "chromosome","start, end: Genomic coordinates of the segment"
    "gene","Gene(s) overlapping the segment."
    "log2","Mean log2 ratio of the segment."
    "probes","Mean log2 ratio of the segment."
    "depth","Average read depth."
    "weight","Reliability weight."
    "p_value","Statistical confidence (lower = more significant)."

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