<tool id="prince" name="VNTR copy number approximation" version="1.1.0">
    <description>Calculates CNV of genomic data based on template</description>
    <requirements>
        <requirement type="package" version="1.2">prince</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        prince -tf "$input1" -to "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="txt" />
    </inputs>
    <outputs>
        <data name="output1" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="prince_input.txt"/>
            <output name="output1" file="prince_output.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        usage: prince [-h] [-bo BOOST_OUTPUT] [-to TARGET_OUTPUT] [-tmp TEMPLATES] [-tf TARGET_FILE] [-bf BOOSTING_FILE] [-k K] [-cn COPYNUMBER]

	Prince Options.

	optional arguments:
	  -h, --help            Show this help message and exit
	  -bo, --boost_output   Output file for training data / training data used to predict copy numbers for queries
          -to, --target_output  Output file for query copy number predictions
          -tmp, --templates     VNTR templates. Default is for M.TB
          -tf, --target_file    Target genome names in a text file
          -bf, --boosting_file  Training genome file names in a text file
          -k, --k               Kmer size used during read recruitment
          -cn, --copynumber     Copy number used for training genome

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubPythonPRINCE,
  author = {Booth, Julian},
  year = {2018},
  title = {PythonPRINCE},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/WGS-TB/PythonPRINCE},
}</citation>
    </citations>
</tool>