root/galaxy-central/tools/multivariate_stats/kcca.xml

リビジョン 2, 6.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.0">
2  <description> </description>
3  <command interpreter="python">
4    kcca.py
5      --input=$input1
6      --output1=$out_file1
7      --x_cols=$x_cols
8      --y_cols=$y_cols
9      --kernel=$kernelChoice.kernel
10      --features=$features
11      #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot":
12      --sigma=$kernelChoice.sigma
13      --degree="None"
14      --scale="None"
15      --offset="None"
16      --order="None"
17      #elif $kernelChoice.kernel == "polydot":
18      --sigma="None"
19      --degree=$kernelChoice.degree
20      --scale=$kernelChoice.scale
21      --offset=$kernelChoice.offset
22      --order="None"
23      #elif $kernelChoice.kernel == "tanhdot":
24      --sigma="None"
25      --degree="None"
26      --scale=$kernelChoice.scale
27      --offset=$kernelChoice.offset
28      --order="None"
29      #elif $kernelChoice.kernel == "besseldot":
30      --sigma=$kernelChoice.sigma
31      --degree=$kernelChoice.degree
32      --scale="None"
33      --offset="None"
34      --order=$kernelChoice.order
35      #elif $kernelChoice.kernel == "anovadot":
36      --sigma=$kernelChoice.sigma
37      --degree=$kernelChoice.degree
38      --scale="None"
39      --offset="None"
40      --order="None"
41      #else:
42      --sigma="None"
43      --degree="None"
44      --scale="None"
45      --offset="None"
46      --order="None"
47      #end if
48  </command>
49  <inputs>
50    <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
51    <param name="x_cols" label="Select columns containing X variables " type="data_column" data_ref="input1" numerical="True" multiple="true" >
52        <validator type="no_options" message="Please select at least one column."/>
53    </param>
54    <param name="y_cols" label="Select columns containing Y variables " type="data_column" data_ref="input1" numerical="True" multiple="true" >
55        <validator type="no_options" message="Please select at least one column."/>
56    </param>
57    <param name="features" size="10" type="integer" value="2" label="Number of canonical components to return" help="Enter an integer value greater than 0"/>
58    <conditional name="kernelChoice">
59        <param name="kernel" type="select" label="Kernel function">
60            <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option>
61            <option value="polydot">Polynomial</option>
62            <option value="vanilladot">Linear</option>
63            <option value="tanhdot">Hyperbolic</option>
64            <option value="laplacedot">Laplacian</option>
65            <option value="besseldot">Bessel</option>
66            <option value="anovadot">ANOVA Radial Basis Function</option>
67            <option value="splinedot">Spline</option>
68        </param>
69        <when value="vanilladot" />
70        <when value="splinedot" />
71        <when value="rbfdot">
72            <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
73        </when>
74        <when value="laplacedot">
75            <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" />
76        </when>
77        <when value="polydot">
78            <param name="degree" size="10" type="float" value="1" label="degree" />
79            <param name="scale" size="10" type="float" value="1" label="scale" />
80            <param name="offset" size="10" type="float" value="1" label="offset" />
81        </when>
82        <when value="tanhdot">
83            <param name="scale" size="10" type="float" value="1" label="scale" />
84            <param name="offset" size="10" type="float" value="1" label="offset" />
85        </when>
86        <when value="besseldot">
87            <param name="sigma" size="10" type="float" value="1" label="sigma" />
88            <param name="order" size="10" type="float" value="1" label="order" />
89            <param name="degree" size="10" type="float" value="1" label="degree" />
90        </when>
91        <when value="anovadot">
92            <param name="sigma" size="10" type="float" value="1" label="sigma" />
93            <param name="degree" size="10" type="float" value="1" label="degree" />
94        </when>
95    </conditional>   
96  </inputs>
97  <outputs>
98    <data format="input" name="out_file1" metadata_source="input1" />
99  </outputs>
100  <requirements>
101    <requirement type="python-module">rpy</requirement>
102  </requirements>
103  <tests>
104    <test>
105        <param name="input1" value="iris.tabular"/>
106        <param name="x_cols" value="1,2"/>
107        <param name="y_cols" value="3,4"/>
108        <param name="kernel" value="anovadot"/>
109        <param name="features" value="4"/>
110        <param name="sigma" value="0.1"/>
111        <param name="degree" value="2"/>
112        <output name="out_file1" file="kcca_out1.tabular" compare="re_match"/>
113    </test>
114    <test>
115        <param name="input1" value="iris.tabular"/>
116        <param name="x_cols" value="3,4"/>
117        <param name="y_cols" value="1,2"/>
118        <param name="kernel" value="rbfdot"/>
119        <param name="features" value="2"/>
120        <param name="sigma" value="0.5"/>
121        <output name="out_file1" file="kcca_out2.tabular" compare="re_match"/>
122    </test>
123  </tests>
124  <help>
125
126
127.. class:: infomark
128
129**TIP:** If your data is not TAB delimited, use *Edit Queries-&gt;Convert characters*
130
131-----
132
133.. class:: infomark
134
135**What it does**
136
137This tool uses functions from 'kernlab' library from R statistical package to perform Kernel Canonical Correlation Analysis (kCCA) on the input data.
138
139*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/*
140
141-----
142
143.. class:: warningmark
144
145**Note**
146
147This 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.
148
149  </help>
150</tool>
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