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comparison kpca.xml @ 0:ffcdde989859 draft

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author iuc
date Tue, 29 Jul 2014 06:30:45 -0400
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1 <tool id="kpca1" name="Kernel Principal Component Analysis" version="1.1.0">
2 <description> </description>
3 <expand macro="requirements" />
4 <macros>
5 <import>statistic_tools_macros.xml</import>
6 </macros>
7 <command interpreter="python">
8 kpca.py
9 --input=$input1
10 --output1=$out_file1
11 --output2=$out_file2
12 --var_cols=$var_cols
13 --kernel=$kernelChoice.kernel
14 --features=$features
15 #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot":
16 --sigma=$kernelChoice.sigma
17 --degree="None"
18 --scale="None"
19 --offset="None"
20 --order="None"
21 #elif $kernelChoice.kernel == "polydot":
22 --sigma="None"
23 --degree=$kernelChoice.degree
24 --scale=$kernelChoice.scale
25 --offset=$kernelChoice.offset
26 --order="None"
27 #elif $kernelChoice.kernel == "tanhdot":
28 --sigma="None"
29 --degree="None"
30 --scale=$kernelChoice.scale
31 --offset=$kernelChoice.offset
32 --order="None"
33 #elif $kernelChoice.kernel == "besseldot":
34 --sigma=$kernelChoice.sigma
35 --degree=$kernelChoice.degree
36 --scale="None"
37 --offset="None"
38 --order=$kernelChoice.order
39 #elif $kernelChoice.kernel == "anovadot":
40 --sigma=$kernelChoice.sigma
41 --degree=$kernelChoice.degree
42 --scale="None"
43 --offset="None"
44 --order="None"
45 #else:
46 --sigma="None"
47 --degree="None"
48 --scale="None"
49 --offset="None"
50 --order="None"
51 #end if
52 </command>
53 <inputs>
54 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
55 <param name="var_cols" label="Select columns containing input variables " type="data_column" data_ref="input1" numerical="True" multiple="true" >
56 <validator type="no_options" message="Please select at least one column."/>
57 </param>
58 <param name="features" size="10" type="integer" value="2" label="Number of principal components to return" help="To return all, enter 0"/>
59 <conditional name="kernelChoice">
60 <param name="kernel" type="select" label="Kernel function">
61 <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option>
62 <option value="polydot">Polynomial</option>
63 <option value="vanilladot">Linear</option>
64 <option value="tanhdot">Hyperbolic</option>
65 <option value="laplacedot">Laplacian</option>
66 <option value="besseldot">Bessel</option>
67 <option value="anovadot">ANOVA Radial Basis Function</option>
68 <option value="splinedot">Spline</option>
69 </param>
70 <when value="vanilladot" />
71 <when value="splinedot" />
72 <when value="rbfdot">
73 <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
74 </when>
75 <when value="laplacedot">
76 <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
77 </when>
78 <when value="polydot">
79 <param name="degree" size="10" type="integer" value="1" label="degree" />
80 <param name="scale" size="10" type="integer" value="1" label="scale" />
81 <param name="offset" size="10" type="integer" value="1" label="offset" />
82 </when>
83 <when value="tanhdot">
84 <param name="scale" size="10" type="integer" value="1" label="scale" />
85 <param name="offset" size="10" type="integer" value="1" label="offset" />
86 </when>
87 <when value="besseldot">
88 <param name="sigma" size="10" type="integer" value="1" label="sigma" />
89 <param name="order" size="10" type="integer" value="1" label="order" />
90 <param name="degree" size="10" type="integer" value="1" label="degree" />
91 </when>
92 <when value="anovadot">
93 <param name="sigma" size="10" type="integer" value="1" label="sigma" />
94 <param name="degree" size="10" type="integer" value="1" label="degree" />
95 </when>
96 </conditional>
97 </inputs>
98 <outputs>
99 <data format="input" name="out_file1" metadata_source="input1" />
100 <data format="pdf" name="out_file2" />
101 </outputs>
102 <tests>
103 <test>
104 <param name="input1" value="iris.tabular"/>
105 <param name="var_cols" value="1,2,3,4"/>
106 <param name="kernel" value="polydot"/>
107 <param name="features" value="2"/>
108 <param name="offset" value="0"/>
109 <param name="scale" value="1"/>
110 <param name="degree" value="2"/>
111 <output name="out_file1" file="kpca_out1.tabular"/>
112 <output name="out_file2" file="kpca_out2.pdf"/>
113 </test>
114 </tests>
115 <help>
116
117
118 .. class:: infomark
119
120 **TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters*
121
122 -----
123
124 .. class:: infomark
125
126 **What it does**
127
128 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.
129
130 *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/*
131
132 -----
133
134 .. class:: warningmark
135
136 **Note**
137
138 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.
139
140 </help>
141 </tool>