<tool id="cnvkit_sex" name="CNVkit Sex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators_and_zahra"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_filename_file' ./sample.cnr &&
        cnvkit.py sex
            ./sample.cnr      
            --output gene-sex.txt
            $male_reference        
    ]]></command>
     <inputs>
        <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr/cnn file" help="Copy number cnn or copy ratio cnr files" />
        <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
        </inputs>
    <outputs>
        <data name="gene_sex" format="txt" label="${tool.name} on ${on_string}: sample's chromosomal sex" from_work_dir="gene-sex.txt" />
    </outputs>
       <tests>
        <test expect_num_outputs="1">
            <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
            <output name="gene_sex" file="gene-sex.txt" />
        </test>
    </tests>
    <help><![CDATA[
        Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y. 
        The output is a table of the sample name (derived from the filename), inferred sex (string “Female” or “Male”), 
        and log2 ratio value of chromosomes X and Y.
    ]]></help>
    <expand macro="citations" />
</tool>