<tool id="wisecondorx_reference_builder" name="WisecondorX build" version="@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>
        reference
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="requirements"/>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occured" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
    @pipefail@
    #for $num, $file in enumerate($npz_inputs):
        ln -s $file "${num}.npz" &&
    #end for
    WisecondorX newref *.npz reference.npz
        --binsize ${bin}
        --cpus \${GALAXY_SLOTS:-4} &&
    mv reference.npz $npz
    ]]></command>
    <inputs>
        <param name="npz_inputs" type="data" label="npz inputs" multiple="True" format="npz"
               help="Build reference from npz inputs from normal sample (at least 10 samples required)"/>
        <param name="bin" size="9" type="integer" value="100000" label="Bin size in nucleotides"
               help="Bin default value is 100 kb (100000)" />
     </inputs>
    <outputs>
        <data name="npz" format="npz" label="reference_${bin}nt" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="npz_inputs"
                   value="0.ref.npz,1.ref.npz,2.ref.npz,3.ref.npz,4.ref.npz,5.ref.npz,6.ref.npz,7.ref.npz,8.ref.npz,9.ref.npz"/>
            <param name="bin" value="10000" />
            <output name="npz" ftype="npz" file="output_reference.npz" compare="sim_size" delta="10000"/>
        </test>
    </tests>
    <help>
@help@
<![CDATA[
.. class:: infomark

**WisecondorX newref reference_input_dir/*.npz reference_output.npz [--optional arguments]**

Option List::

  --nipt        Always include this flag for the generation of a NIPT reference
  --binsize     Size per bin in bp, defines the resolution of the output (default: x=1e5)
                **Should be a multiple of the 5e3**
  --refsize     Amount of reference locations per target;
                should generally not be tweaked (default: x=300)
  --yfrac       Y read fraction cutoff, in order to manually define gender.
                Setting this to 1 will treat all samples as female.
                This parameter is not currently exposed in the Galaxy wrapper.
  --plotyfrac   plots Y read fraction histogram and Gaussian mixture fit to file x,
                can help when setting --yfrac manually; software quits after plotting
                The --normdup parameter is currently not exposed in this Galaxy
                wrapper. Default is to remove duplicates.
  --cpus        Number of threads requested (This is defined by the Galaxy administrator)

    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gky1263</citation>
    </citations>
</tool>