|
0
|
1 <tool id="generate_matrix_for_pca_and_lda1" name="Generate A Matrix" version="1.0.0">
|
|
|
2 <description>for using PC and LDA</description>
|
|
|
3 <command interpreter="perl">generate_matrix_for_pca_lda.pl $input_1 $input_2 $output</command>
|
|
|
4
|
|
|
5 <inputs>
|
|
|
6 <param format="tabular" name="input_1" type="data" label="Source file First: a matrix (samples/observations in rows and variables/features in columns)"> </param>
|
|
|
7 <param format="tabular" name="input_2" type="data" label="Source file Second: a table (samples/observations with response/class label)"> </param>
|
|
|
8 </inputs>
|
|
|
9
|
|
|
10 <outputs>
|
|
|
11 <data format="tabular" name="output" />
|
|
|
12 </outputs>
|
|
|
13
|
|
|
14 <tests>
|
|
|
15 <test>
|
|
|
16 <param name="input_1" value="matrix_generator_for_pc_and_lda_input_1.tabular"/>
|
|
|
17 <param name="input_2" value="matrix_generator_for_pc_and_lda_input_2.tabular"/>
|
|
|
18 <output name="output" file="matrix_generator_for_pc_and_lda_output.tabular"/>
|
|
|
19 </test>
|
|
|
20 </tests>
|
|
|
21
|
|
|
22 <help>
|
|
|
23
|
|
|
24 .. class:: infomark
|
|
|
25
|
|
|
26 **What it does**
|
|
|
27
|
|
|
28 This tool consists of a module to generate a matrix to be used for running the Linear Discriminant Analysis as described in Carrel et al., 2006 (PMID: 17009873)
|
|
|
29
|
|
|
30 *Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome. PLoS Genet 2(9): e151. doi:10.1371/journal.pgen.0020151*
|
|
|
31
|
|
|
32 -----
|
|
|
33
|
|
|
34 **Example**
|
|
|
35
|
|
|
36 - Input file (Source file First)
|
|
|
37
|
|
|
38 .. image:: tools/lda/first_matrix_generator_example_file.png
|
|
|
39
|
|
|
40
|
|
|
41 - Input file (Source file Second)
|
|
|
42
|
|
|
43 .. image:: tools/lda/second_matrix_generator_example_file.png
|
|
|
44
|
|
|
45
|
|
|
46 </help>
|
|
|
47
|
|
|
48 </tool>
|
