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author jowong
date Mon, 19 Nov 2018 04:19:54 -0500
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1 <tool id="kwip" name="kwip" version="1.1.0">
2 <description>Calculates CNV of genomic data based on template</description>
3 <requirements>
4 <requirement type="package" version="0.2.0">kwip</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 kwip -h
8 ]]></command>
9 <inputs>
10 <param type="data" name="input1" format="txt" />
11 </inputs>
12 <outputs>
13 <data name="output1" format="txt" />
14 </outputs>
15 <tests>
16 <test>
17 <param name="input1" value="prince_input.txt"/>
18 <output name="output1" file="prince_output.txt"/>
19 </test>
20 </tests>
21 <help><![CDATA[
22 usage: prince [-h] [-bo BOOST_OUTPUT] [-to TARGET_OUTPUT] [-tmp TEMPLATES] [-tf TARGET_FILE] [-bf BOOSTING_FILE] [-k K] [-cn COPYNUMBER]
23
24 Prince Options.
25
26 optional arguments:
27 -h, --help Show this help message and exit
28 -bo, --boost_output Output file for training data / training data used to predict copy numbers for queries
29 -to, --target_output Output file for query copy number predictions
30 -tmp, --templates VNTR templates. Default is for M.TB
31 -tf, --target_file Target genome names in a text file
32 -bf, --boosting_file Training genome file names in a text file
33 -k, --k Kmer size used during read recruitment
34 -cn, --copynumber Copy number used for training genome
35
36 ]]></help>
37 <citations>
38 <citation type="bibtex">
39 @misc{githubPythonPRINCE,
40 author = {Booth, Julian},
41 year = {2018},
42 title = {PythonPRINCE},
43 publisher = {GitHub},
44 journal = {GitHub repository},
45 url = {https://github.com/WGS-TB/PythonPRINCE},
46 }</citation>
47 </citations>
48 </tool>