|
10
|
1 <tool id="kwip" name="kwip" version="1.1.9">
|
|
7
|
2 <description>Calculates k-mer weighted inner product, a de novo estimator of genetic similarity</description>
|
|
0
|
3 <requirements>
|
|
|
4 <requirement type="package" version="0.2.0">kwip</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command detect_errors="exit_code"><![CDATA[
|
|
10
|
7 kwip -h
|
|
0
|
8 ]]></command>
|
|
|
9 <inputs>
|
|
2
|
10 <param name="inputs" format="data" type="data_collection" label="inputs" help="Specify dataset with hashed reads"/>
|
|
1
|
11 <section name="advanced" title="Advanced options" expanded="false">
|
|
2
|
12 <param type="boolean" argument="--unweighted" label="Unweighted Inner Product" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/>
|
|
1
|
13 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
|
|
|
14
|
|
|
15 </section>
|
|
0
|
16 </inputs>
|
|
|
17 <outputs>
|
|
7
|
18 <data name="kwip_kernel" label="kWip kernel" format="txt" type="data" from_work_dir="kwip.kernel"/>
|
|
|
19 <data name="kwip_distance" label="kWip distance" format="txt" type="data" from_work_dir="kwip.dist"/>
|
|
0
|
20 </outputs>
|
|
|
21 <tests>
|
|
|
22 </tests>
|
|
|
23 <help><![CDATA[
|
|
1
|
24 usage: USAGE: kwip [options] hashes
|
|
0
|
25
|
|
1
|
26 kWip Options.
|
|
0
|
27
|
|
|
28 optional arguments:
|
|
1
|
29 -t, --threads Number of threads to utilise. [default N_CPUS]
|
|
|
30 -k, --kernel Output file for the kernel matrix. [default None]
|
|
|
31 -d, --distance Output file for the distance matrix. [default stdout]
|
|
|
32 -U, --unweighted Use the unweighted inner proudct kernel. [default off]
|
|
|
33 -w, --weights Bin weight vector file (input, or output w/ -C).
|
|
|
34 -C, --calc-weights Calculate only the bin weight vector, not kernel matrix.
|
|
|
35 -h, --help Print this help message.
|
|
|
36 -V, --version Print the version string.
|
|
|
37 -v, --verbose Increase verbosity. May or may not acutally do anything.
|
|
|
38 -q, --quiet Execute silently but for errors.
|
|
|
39
|
|
|
40 Each sample's oxli Countgraph should be specified after arguments:
|
|
|
41 kwip [options] sample1.ct sample2.ct ... sampleN.ct
|
|
0
|
42
|
|
|
43 ]]></help>
|
|
|
44 <citations>
|
|
|
45 <citation type="bibtex">
|
|
|
46 @misc{githubPythonPRINCE,
|
|
1
|
47 author = {Murray, Kevin},
|
|
|
48 year = {2015},
|
|
|
49 title = {kWIP},
|
|
0
|
50 publisher = {GitHub},
|
|
|
51 journal = {GitHub repository},
|
|
1
|
52 url = {https://github.com/kdmurray91/kWIPE},
|
|
0
|
53 }</citation>
|
|
|
54 </citations>
|
|
|
55 </tool>
|
