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<tool id="abims_ACP" name="PCA" version="1.2">

    <description>Principal Component Analysis using FactoMineR</description>

    <command interpreter="Rscript">
        abims_acp.r file "$input" graph TRUE scale.unit "$scale_unit" sep "$sep" dec "$dec"
    </command> 

    <inputs>
        <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
        <!--<param name="graph" type="select" label="graph" help="if FALSE no graph generated">
            <option value="T" selected="true">TRUE</option>
            <option value="F" >FALSE</option>
        </param>-->
        <param name="scale_unit" type="select" label="scale.unit" help="if FALSE no reduction of variables">
            <option value="T" selected="true">TRUE</option>
            <option value="F" >FALSE</option>
        </param>
        
        <param name="sep" type="select" format="text" optional="true">
		<label>Separator of columns</label>
		<option value="tabulation">tabulation</option>
		<option value="semicolon">;</option>
		<option value="comma">,</option>
	</param>
        <param name="dec" type="text" label="Decimal separator" value="." help="" />
         
        <!--<param name="nr_col_names" type="integer" label="names" value="2" help="number of the column with names of metabolits" />
        <param name="from" type="integer" label="from" value="15" help="number of the column starting peak values data (to exlude all metadata)" />
        <param name="to" type="integer" label="to" value="30" help="number of the column finishing peak values data (to exlude all metadata)" />
        <param name="gr_number" type="integer" label="gr_number" value="2" help="number of groups (conditions)" />
        <param name="nb_col_gr" type="text" label="nb_col_gr" value="8,8" help="number of column of each group; separate with coma as indicated; first position coresponding to the first group etc." />
        <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />-->
        
    </inputs>

    <outputs>
        <data name="acp_zip" format="zip" from_work_dir="acp.zip" label="${input.name[:-4]}.pca.zip"/>
    </outputs>

    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <help>

	
.. class:: infomark

**Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 

---------------------------------------------------

===
PCA
===

-----------
Description
-----------


Performs **Principal Component Analysis (PCA)** with supplementary individuals, supplementary quantitative variables and supplementary categorical variables.
Missing values are replaced by the column mean. This scripts uses the FactoMineR package.


-----------
Input files
-----------

+---------------------------+------------+
| Parameter : num + label   |   Format   |
+===========================+============+
| 1 : Data Matrix file      | Tabular    |
+---------------------------+------------+



----------
Parameters
----------

**Data Matrix file**

Matrix of numeric data with headers (tabular format) issued from diffreport or annotateDiffreport to make post xcms analyse  . 

**scale.unit**

If FALSE: no reduction of the variables

**Separator of columns:**

Type of separator for the columns

**Decimal separator:**

Type of decimal separator of the numbers in your tabular files.



------------
Output files
------------



**input_name.pca.zip**

	| A zip file containing fours files (eigenvalue.png, percentage_of_variance.png, Rplots.pdf and Rplots1.pdf).
	

---------------------------------------------------



---------------
Working example
---------------


Input files
-----------

**>A part of an example of Data Matrix file input :**
	

+--------+------------------+----------------+
| Name   | AN7              | AN8            |	                                       
+========+==================+================+
|M102T645| 10880.0637170802 |17207.2222120537|
+--------+------------------+----------------+
|M105T604| 41911.160863452  |38105.7953589089|  
+--------+------------------+----------------+       



Parameters
----------

| scale.unit -> **TRUE*
| Separator of columns: -> **tabulation**
| Decimal separator -> **.**
	
	

Output files
------------


**eigenvalue.png:**

.. image:: pca_abims_eigenvalue.png

**percentage_of_variance.png:**

.. image:: pca_abims_percentage_of_variance.png

**Rplots.pdf:**

.. image:: pca_abims_Rplots.png

**Rplots1.pdf:**

.. image:: pca_abims_Rplots1.png


	

    </help>

</tool>