<tool id="kwip" name="kwip" version="1.1.1">
    <description>Calculates CNV of genomic data based on template</description>
    <requirements>
        <requirement type="package" version="0.2.0">kwip</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        kwip 
        -t $advanced.thread 
        -k kwip.kernel 
        -d kwip.dist 
        $advanced.unweighted
        #if str( $advanced.calc ) == "True"
            -w $advanced.weight -C
        #end if 
        #for $path in $paths# $path #end for#
    ]]></command>
    <inputs>
        <param name="input" format="data" type="data_collection" label="input" help="Specify dataset with hashed reads"/>
        <section name="advanced" title="Advanced options" expanded="false">
            <param type="boolean" argument="--unweighted" label="Small count" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/>
            <param type="boolean" name="calc" label="Calculate only the bin weight vector, not kernel matrix." help="Calculate only the bin weight vector, not kernel matrix with bin weight vector file" truevalue="True" falsevalue="False" checked="false" />
            <param type="data" name="weight" label="Bin weight vector file" help="Bin weight vector file (input, or output w/ -C)." />
            <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />

        </section>
    </inputs>
    <outputs>
        <data name="kwip_kernel" label="kWip kernel" format="data" from_work_dir="kwip.kernel"/>
        <data name="kwip_distance" label="kWip distance" format="data" from_work_dir="kwip.dist"/>
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[
        usage: USAGE: kwip [options] hashes

	kWip Options.

	optional arguments:
          -t, --threads       Number of threads to utilise. [default N_CPUS]
          -k, --kernel        Output file for the kernel matrix. [default None]
          -d, --distance      Output file for the distance matrix. [default stdout]
          -U, --unweighted    Use the unweighted inner proudct kernel. [default off]
          -w, --weights       Bin weight vector file (input, or output w/ -C).
          -C, --calc-weights  Calculate only the bin weight vector, not kernel matrix.
          -h, --help          Print this help message.
          -V, --version       Print the version string.
          -v, --verbose       Increase verbosity. May or may not acutally do anything.
          -q, --quiet         Execute silently but for errors.

          Each sample's oxli Countgraph should be specified after arguments:
          kwip [options] sample1.ct sample2.ct ... sampleN.ct

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubPythonPRINCE,
  author = {Murray, Kevin},
  year = {2015},
  title = {kWIP},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/kdmurray91/kWIPE},
}</citation>
    </citations>
</tool>