<tool id="wisecondorx_npz_converter" name="WisecondorX convert" version="@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>
        bam to npz
    </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@
    ln -f -s $bam.metadata.bam_index input.bam.bai &&
    ln -f -s $bam input.bam &&
    printf "Creating 5kb bins for file $bam.element_identifier" &&
    WisecondorX convert input.bam output.npz
    ]]></command>
    <inputs>
        <param name="bam" type="data" label="Bam input" format="bam"
               help="input Bam is converted in .npz file"/>
     </inputs>
    <outputs>
        <data name="npz" format="npz" from_work_dir="output.npz" label="${on_string}.npz" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param ftype="bam" name="bam" value="npz_convert_input.bam" />
            <output name="npz" ftype="npz" file="npz_convert_output.npz" compare="sim_size" delta="10000"/>
        </test>
    </tests>
    <help>
@help@
<![CDATA[
.. class:: infomark

**WisecondorX convert input.bam/cram output.npz [--optional arguments]**

Option List::

  --reference   Fasta reference to be used with cram inputs.
                This option is currently not available in this Galaxy wrapper,
                which takes only bam inputs.
  --binsize     Size per bin in bp; the reference bin size should be a multiple of this value.
                Note that this parameter does not impact the resolution, yet it
                can be used to optimize processing speed (default: x=5e3).
                The --binsize parameter is currently not exposed in this Galaxy
                wrapper and is fixed to 5e3
  --normdup     Use this flag to avoid duplicate removal.
                The --normdup parameter is currently not exposed in this Galaxy
                wrapper. Default is to remove duplicates.

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