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comparison kpca.xml @ 1:2e7bc1bb2dbe draft default tip

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author iuc
date Fri, 09 Jan 2015 12:56:07 -0500
parents ffcdde989859
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0:ffcdde989859 1:2e7bc1bb2dbe
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>statistic_tools_macros.xml</import> 5 <import>statistic_tools_macros.xml</import>
6 </macros> 6 </macros>
7 <command interpreter="python"> 7 <command interpreter="python">
8 kpca.py 8 <![CDATA[
9 kpca.py
9 --input=$input1 10 --input=$input1
10 --output1=$out_file1 11 --output1=$out_file1
11 --output2=$out_file2 12 --output2=$out_file2
12 --var_cols=$var_cols 13 --var_cols=$var_cols
13 --kernel=$kernelChoice.kernel 14 --kernel=$kernelChoice.kernel
47 --degree="None" 48 --degree="None"
48 --scale="None" 49 --scale="None"
49 --offset="None" 50 --offset="None"
50 --order="None" 51 --order="None"
51 #end if 52 #end if
53 ]]>
52 </command> 54 </command>
53 <inputs> 55 <inputs>
54 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> 56 <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" > 57 <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."/> 58 <validator type="no_options" message="Please select at least one column."/>
91 </when> 93 </when>
92 <when value="anovadot"> 94 <when value="anovadot">
93 <param name="sigma" size="10" type="integer" value="1" label="sigma" /> 95 <param name="sigma" size="10" type="integer" value="1" label="sigma" />
94 <param name="degree" size="10" type="integer" value="1" label="degree" /> 96 <param name="degree" size="10" type="integer" value="1" label="degree" />
95 </when> 97 </when>
96 </conditional> 98 </conditional>
97 </inputs> 99 </inputs>
98 <outputs> 100 <outputs>
99 <data format="input" name="out_file1" metadata_source="input1" /> 101 <data format="input" name="out_file1" metadata_source="input1" />
100 <data format="pdf" name="out_file2" /> 102 <data format="pdf" name="out_file2" />
101 </outputs> 103 </outputs>
111 <output name="out_file1" file="kpca_out1.tabular"/> 113 <output name="out_file1" file="kpca_out1.tabular"/>
112 <output name="out_file2" file="kpca_out2.pdf"/> 114 <output name="out_file2" file="kpca_out2.pdf"/>
113 </test> 115 </test>
114 </tests> 116 </tests>
115 <help> 117 <help>
118 <![CDATA[
116 119
117 120
118 .. class:: infomark 121 .. class:: infomark
119 122
120 **TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters* 123 **TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters*
121 124
122 ----- 125 -----
123 126
124 .. class:: infomark 127 .. class:: infomark
125 128
126 **What it does** 129 **What it does**
127 130
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. 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.
129 132
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/* 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/*
131 134
132 ----- 135 -----
133 136
135 138
136 **Note** 139 **Note**
137 140
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. 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.
139 142
143 ]]>
140 </help> 144 </help>
141 </tool> 145 </tool>