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1 <tool id="kwip" name="kwip" version="1.1.0">
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2 <description>Calculates CNV of genomic data based on template</description>
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3 <requirements>
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4 <requirement type="package" version="0.2.0">kwip</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 kwip -h
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="input1" format="txt" />
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11 </inputs>
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12 <outputs>
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13 <data name="output1" format="txt" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input1" value="prince_input.txt"/>
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18 <output name="output1" file="prince_output.txt"/>
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19 </test>
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20 </tests>
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21 <help><![CDATA[
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22 usage: prince [-h] [-bo BOOST_OUTPUT] [-to TARGET_OUTPUT] [-tmp TEMPLATES] [-tf TARGET_FILE] [-bf BOOSTING_FILE] [-k K] [-cn COPYNUMBER]
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23
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24 Prince Options.
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25
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26 optional arguments:
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27 -h, --help Show this help message and exit
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28 -bo, --boost_output Output file for training data / training data used to predict copy numbers for queries
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29 -to, --target_output Output file for query copy number predictions
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30 -tmp, --templates VNTR templates. Default is for M.TB
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31 -tf, --target_file Target genome names in a text file
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32 -bf, --boosting_file Training genome file names in a text file
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33 -k, --k Kmer size used during read recruitment
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34 -cn, --copynumber Copy number used for training genome
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35
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36 ]]></help>
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37 <citations>
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38 <citation type="bibtex">
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39 @misc{githubPythonPRINCE,
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40 author = {Booth, Julian},
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41 year = {2018},
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42 title = {PythonPRINCE},
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43 publisher = {GitHub},
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44 journal = {GitHub repository},
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45 url = {https://github.com/WGS-TB/PythonPRINCE},
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46 }</citation>
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47 </citations>
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48 </tool>
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