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comparison pca.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 pca.py 8 <![CDATA[
9 pca.py
9 $input1 10 $input1
10 $var_cols 11 $var_cols
11 $methodChoice.method 12 $methodChoice.method
12 $out_file1 13 $out_file1
13 $out_file2 14 $out_file2
14 #if $methodChoice.method == "svd": 15 #if $methodChoice.method == "svd":
15 $methodChoice.scale 16 $methodChoice.scale
16 #end if 17 #end if
18 ]]>
17 </command> 19 </command>
18 <inputs> 20 <inputs>
19 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> 21 <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/>
20 <param name="var_cols" label="Select columns containing input variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > 22 <param name="var_cols" label="Select columns containing input variables " type="data_column" data_ref="input1" numerical="True" multiple="true" >
21 <validator type="no_options" message="Please select at least one column."/> 23 <validator type="no_options" message="Please select at least one column."/>
32 <param name="scale" type="select" label="Centering and Scaling" help="Can be used to center and/or scale variables"> 34 <param name="scale" type="select" label="Centering and Scaling" help="Can be used to center and/or scale variables">
33 <option value="none" selected="true">None</option> 35 <option value="none" selected="true">None</option>
34 <option value="center">Center only</option> 36 <option value="center">Center only</option>
35 <option value="scale">Scale only</option> 37 <option value="scale">Scale only</option>
36 <option value="both">Center and Scale</option> 38 <option value="both">Center and Scale</option>
37 </param> 39 </param>
38 </when> 40 </when>
39 </conditional> 41 </conditional>
40 </inputs> 42 </inputs>
41 <outputs> 43 <outputs>
42 <data format="input" name="out_file1" metadata_source="input1" /> 44 <data format="input" name="out_file1" metadata_source="input1" />
65 <output name="out_file1" file="pca_out5.tabular"/> 67 <output name="out_file1" file="pca_out5.tabular"/>
66 <output name="out_file2" file="pca_out6.pdf"/> 68 <output name="out_file2" file="pca_out6.pdf"/>
67 </test> 69 </test>
68 </tests> 70 </tests>
69 <help> 71 <help>
72 <![CDATA[
70 73
71 74
72 .. class:: infomark 75 .. class:: infomark
73 76
74 **TIP:** If your data is not TAB delimited, use *Edit Datasets-&gt;Convert characters* 77 **TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters*
75 78
76 ----- 79 -----
77 80
78 .. class:: infomark 81 .. class:: infomark
79 82
80 **What it does** 83 **What it does**
81 84
82 This tool performs Principal Component Analysis on the given numeric input data using functions from R statistical package - 'princomp' function (for Eigenvector based solution) and 'prcomp' function (for Singular value decomposition based solution). It outputs two files, one containing the summary statistics of PCA, and the other containing biplots of the observations and principal components. 85 This tool performs Principal Component Analysis on the given numeric input data using functions from R statistical package - 'princomp' function (for Eigenvector based solution) and 'prcomp' function (for Singular value decomposition based solution). It outputs two files, one containing the summary statistics of PCA, and the other containing biplots of the observations and principal components.
83 86
84 *R Development Core Team (2009). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.* 87 *R Development Core Team (2009). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.*
85 88
86 ----- 89 -----
87 90
95 98
96 - Std. deviation: Standard deviations of the principal components 99 - Std. deviation: Standard deviations of the principal components
97 - Loadings: a list of eigen-vectors/variable loadings 100 - Loadings: a list of eigen-vectors/variable loadings
98 - Scores: Scores of the input data on the principal components 101 - Scores: Scores of the input data on the principal components
99 102
103 ]]>
100 </help> 104 </help>
101 </tool> 105 </tool>