<tool id="cnvkit_export_bed" name="CNVkit Export BED" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Converts the Segmented copy ratio data file (*.cns) file into BED file</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 bed
            ./sample.cns
            $advanced_settings.label_genes
            #if $advanced_settings.sample_id
              --sample-id '$advanced_settings.sample_id'
            #end if
            #if $advanced_settings.ploidy
              --ploidy $advanced_settings.ploidy
            #end if
            #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
              --sample-sex '$advanced_settings.sample_sex'
            #end if
            $advanced_settings.male_reference  
            --output sample.cnv.bed
            #if $advanced_settings.diploid_parx_genome
              --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
            #end if
    ]]></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="--label-genes" type="boolean" checked="false" truevalue="--label-genes" falsevalue="" label="Label Genes" help="Show gene names in the 4th column of the BED file" />
            <param argument="--sample-id" type="text" label="Sample ID" help="Sample name to write in the genotype field of the output VCF file" />
            <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
            <expand macro="sample_sex"/>
            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Male Reference" help="Assume inputs were normalized to a male reference" />
            <param argument="--diploid-parx-genome" type="text" label="Diploid Parx Genome" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
        </section>  
        </inputs>
    <outputs>
        <data name="CNVs_BED" format="bed" label="${tool.name} on ${on_string}: CNVs BED file" from_work_dir="sample.cnv.bed" />
    </outputs>
       <tests>
        <test expect_num_outputs="1">
            <param name="input_segmented_file" ftype="cns" value="sample.cns" />
            <param name="sample_id" value="SampleID" />
            <param name="sample_sex" value="Female" />
            <output name="CNVs_BED" file="sample.cnv.bed" />
        </test>
    </tests>
    <help><![CDATA[

Export the segmented copy number data (from a .cns file) to BED format. 
The resulting BED file describes copy number gains and losses across each segment.
-----

**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>