|
1
|
1 <tool id="kwip" name="kwip" version="1.1.1">
|
|
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[
|
|
1
|
7 kwip
|
|
|
8 -t $advanced.thread
|
|
|
9 -k kwip.kernel
|
|
|
10 -d kwip.dist
|
|
|
11 $advanced.unweighted
|
|
|
12 #if str( $advanced.calc ) == "True"
|
|
|
13 -w $advanced.weight -C
|
|
|
14 #end if
|
|
|
15 #for $path in $paths# $path #end for#
|
|
0
|
16 ]]></command>
|
|
|
17 <inputs>
|
|
1
|
18 <param name="input" format="data" type="data_collection" label="input" help="Specify dataset with hashed reads"/>
|
|
|
19 <section name="advanced" title="Advanced options" expanded="false">
|
|
|
20 <param type="boolean" argument="--unweighted" label="Small count" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/>
|
|
|
21 <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" />
|
|
|
22 <param type="data" name="weight" label="Bin weight vector file" help="Bin weight vector file (input, or output w/ -C)." />
|
|
|
23 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
|
|
|
24
|
|
|
25 </section>
|
|
0
|
26 </inputs>
|
|
|
27 <outputs>
|
|
1
|
28 <data name="kwip_kernel" label="kWip kernel" format="data" from_work_dir="kwip.kernel"/>
|
|
|
29 <data name="kwip_distance" label="kWip distance" format="data" from_work_dir="kwip.dist"/>
|
|
0
|
30 </outputs>
|
|
|
31 <tests>
|
|
|
32 </tests>
|
|
|
33 <help><![CDATA[
|
|
1
|
34 usage: USAGE: kwip [options] hashes
|
|
0
|
35
|
|
1
|
36 kWip Options.
|
|
0
|
37
|
|
|
38 optional arguments:
|
|
1
|
39 -t, --threads Number of threads to utilise. [default N_CPUS]
|
|
|
40 -k, --kernel Output file for the kernel matrix. [default None]
|
|
|
41 -d, --distance Output file for the distance matrix. [default stdout]
|
|
|
42 -U, --unweighted Use the unweighted inner proudct kernel. [default off]
|
|
|
43 -w, --weights Bin weight vector file (input, or output w/ -C).
|
|
|
44 -C, --calc-weights Calculate only the bin weight vector, not kernel matrix.
|
|
|
45 -h, --help Print this help message.
|
|
|
46 -V, --version Print the version string.
|
|
|
47 -v, --verbose Increase verbosity. May or may not acutally do anything.
|
|
|
48 -q, --quiet Execute silently but for errors.
|
|
|
49
|
|
|
50 Each sample's oxli Countgraph should be specified after arguments:
|
|
|
51 kwip [options] sample1.ct sample2.ct ... sampleN.ct
|
|
0
|
52
|
|
|
53 ]]></help>
|
|
|
54 <citations>
|
|
|
55 <citation type="bibtex">
|
|
|
56 @misc{githubPythonPRINCE,
|
|
1
|
57 author = {Murray, Kevin},
|
|
|
58 year = {2015},
|
|
|
59 title = {kWIP},
|
|
0
|
60 publisher = {GitHub},
|
|
|
61 journal = {GitHub repository},
|
|
1
|
62 url = {https://github.com/kdmurray91/kWIPE},
|
|
0
|
63 }</citation>
|
|
|
64 </citations>
|
|
|
65 </tool>
|
