<tool id="generate_matrix_for_pca_and_lda1" name="Generate A Matrix">
    <description>for using PC and LDA</description>
    <command interpreter="perl">generate_matrix_for_pca_lda.pl $input_1 $input_2 $output</command>

    <inputs>
        <param format="tabular" name="input_1" type="data" label="Source file First: a matrix (samples/observations in rows and variables/features in columns)"> </param>
        <param format="tabular" name="input_2" type="data" label="Source file Second: a table (samples/observations with response/class label)"> </param>
    </inputs>

    <outputs>
        <data format="tabular" name="output" />
    </outputs>

    <tests>
        <test>
            <param name="input_1" value="matrix_generator_for_pc_and_lda_input_1.tabular"/>
            <param name="input_2" value="matrix_generator_for_pc_and_lda_input_2.tabular"/>
            <output name="output" file="matrix_generator_for_pc_and_lda_output.tabular"/>
        </test>
    </tests>

    <help>

.. class:: infomark

**What it does**

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)

*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*

-----

**Example**

- Input file (Source file First)

.. image:: ./static/images/tools/lda/first_matrix_generator_example_file.png


- Input file (Source file Second)

.. image:: ./static/images/tools/lda/second_matrix_generator_example_file.png


</help>

</tool>