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comparison kpca.xml @ 0:5642f7ee948b draft

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author devteam
date Mon, 19 May 2014 11:00:04 -0400
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1 <tool id="kpca1" name="Kernel Principal Component Analysis" version="1.0.0">
2 <description> </description>
3 <requirements>
4 <requirement type="package" version="1.0.3">rpy</requirement>
5 <requirement type="package" version="2.11.0">R</requirement>
6 <requirement type="package" version="0.1-4">kernlab</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="0.7.1">bx-python</requirement>
9 </requirements>
10 <command interpreter="python">
11 kpca.py
12 --input=$input1
13 --output1=$out_file1
14 --output2=$out_file2
15 --var_cols=$var_cols
16 --kernel=$kernelChoice.kernel
17 --features=$features
18 #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot":
19 --sigma=$kernelChoice.sigma
20 --degree="None"
21 --scale="None"
22 --offset="None"
23 --order="None"
24 #elif $kernelChoice.kernel == "polydot":
25 --sigma="None"
26 --degree=$kernelChoice.degree
27 --scale=$kernelChoice.scale
28 --offset=$kernelChoice.offset
29 --order="None"
30 #elif $kernelChoice.kernel == "tanhdot":
31 --sigma="None"
32 --degree="None"
33 --scale=$kernelChoice.scale
34 --offset=$kernelChoice.offset
35 --order="None"
36 #elif $kernelChoice.kernel == "besseldot":
37 --sigma=$kernelChoice.sigma
38 --degree=$kernelChoice.degree
39 --scale="None"
40 --offset="None"
41 --order=$kernelChoice.order
42 #elif $kernelChoice.kernel == "anovadot":
43 --sigma=$kernelChoice.sigma
44 --degree=$kernelChoice.degree
45 --scale="None"
46 --offset="None"
47 --order="None"
48 #else:
49 --sigma="None"
50 --degree="None"
51 --scale="None"
52 --offset="None"
53 --order="None"
54 #end if
55 </command>
56 <inputs>
57 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
58 <param name="var_cols" label="Select columns containing input variables " type="data_column" data_ref="input1" numerical="True" multiple="true" >
59 <validator type="no_options" message="Please select at least one column."/>
60 </param>
61 <param name="features" size="10" type="integer" value="2" label="Number of principal components to return" help="To return all, enter 0"/>
62 <conditional name="kernelChoice">
63 <param name="kernel" type="select" label="Kernel function">
64 <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option>
65 <option value="polydot">Polynomial</option>
66 <option value="vanilladot">Linear</option>
67 <option value="tanhdot">Hyperbolic</option>
68 <option value="laplacedot">Laplacian</option>
69 <option value="besseldot">Bessel</option>
70 <option value="anovadot">ANOVA Radial Basis Function</option>
71 <option value="splinedot">Spline</option>
72 </param>
73 <when value="vanilladot" />
74 <when value="splinedot" />
75 <when value="rbfdot">
76 <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
77 </when>
78 <when value="laplacedot">
79 <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
80 </when>
81 <when value="polydot">
82 <param name="degree" size="10" type="integer" value="1" label="degree" />
83 <param name="scale" size="10" type="integer" value="1" label="scale" />
84 <param name="offset" size="10" type="integer" value="1" label="offset" />
85 </when>
86 <when value="tanhdot">
87 <param name="scale" size="10" type="integer" value="1" label="scale" />
88 <param name="offset" size="10" type="integer" value="1" label="offset" />
89 </when>
90 <when value="besseldot">
91 <param name="sigma" size="10" type="integer" value="1" label="sigma" />
92 <param name="order" size="10" type="integer" value="1" label="order" />
93 <param name="degree" size="10" type="integer" value="1" label="degree" />
94 </when>
95 <when value="anovadot">
96 <param name="sigma" size="10" type="integer" value="1" label="sigma" />
97 <param name="degree" size="10" type="integer" value="1" label="degree" />
98 </when>
99 </conditional>
100 </inputs>
101 <outputs>
102 <data format="input" name="out_file1" metadata_source="input1" />
103 <data format="pdf" name="out_file2" />
104 </outputs>
105 <tests>
106 <test>
107 <param name="input1" value="iris.tabular"/>
108 <param name="var_cols" value="1,2,3,4"/>
109 <param name="kernel" value="polydot"/>
110 <param name="features" value="2"/>
111 <param name="offset" value="0"/>
112 <param name="scale" value="1"/>
113 <param name="degree" value="2"/>
114 <output name="out_file1" file="kpca_out1.tabular"/>
115 <output name="out_file2" file="kpca_out2.pdf"/>
116 </test>
117 </tests>
118 <help>
119
120
121 .. class:: infomark
122
123 **TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters*
124
125 -----
126
127 .. class:: infomark
128
129 **What it does**
130
131 This tool uses functions from 'kernlab' library from R statistical package to perform Kernel Principal Component Analysis (kPCA) on the input data. It outputs two files, one containing the summary statistics of the performed kPCA, and the other containing a scatterplot matrix of rotated values reported by kPCA.
132
133 *Alexandros Karatzoglou, Alex Smola, Kurt Hornik, Achim Zeileis (2004). kernlab - An S4 Package for Kernel Methods in R. Journal of Statistical Software 11(9), 1-20. URL http://www.jstatsoft.org/v11/i09/*
134
135 -----
136
137 .. class:: warningmark
138
139 **Note**
140
141 This tool currently treats all variables as continuous numeric variables. Running the tool on categorical variables might result in incorrect results. Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis.
142
143 </help>
144 </tool>