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1 <tool id="generate_matrix_for_pca_and_lda1" name="Generate A Matrix" version="1.0.0">
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2 <description>for using PC and LDA</description>
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3 <command interpreter="perl">generate_matrix_for_pca_lda.pl $input_1 $input_2 $output</command>
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4
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5 <inputs>
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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>
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7 <param format="tabular" name="input_2" type="data" label="Source file Second: a table (samples/observations with response/class label)"> </param>
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8 </inputs>
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9
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10 <outputs>
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11 <data format="tabular" name="output" />
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12 </outputs>
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13
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14 <tests>
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15 <test>
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16 <param name="input_1" value="matrix_generator_for_pc_and_lda_input_1.tabular"/>
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17 <param name="input_2" value="matrix_generator_for_pc_and_lda_input_2.tabular"/>
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18 <output name="output" file="matrix_generator_for_pc_and_lda_output.tabular"/>
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19 </test>
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20 </tests>
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21
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22 <help>
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23
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24 .. class:: infomark
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25
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26 **What it does**
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27
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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)
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29
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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*
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31
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32 -----
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33
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34 **Example**
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35
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36 - Input file (Source file First)
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37
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38 .. image:: tools/lda/first_matrix_generator_example_file.png
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39
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40
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41 - Input file (Source file Second)
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42
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43 .. image:: tools/lda/second_matrix_generator_example_file.png
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44
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45
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46 </help>
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47
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48 </tool>
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