<tool id="intens_check" name="Intensity Check" version="1.0.1">
	<description>Adding informations about intensities in the Variable metadata</description>
	<requirements>
	<requirement type="package" version="1.1_4">r-batch</requirement>
	</requirements>
	<command interpreter="Rscript">
  
		wrapper_intensity_check.R
	
		dataMatrix_in "$dataMatrix_in"
		sampleMetadata_in "$sampleMetadata_in"
		variableMetadata_in "$variableMetadata_in"
	
		class_col "$class_col"
	
		type "${type_cond.type}"
		#if $type_cond.type == "One_class" :
		class1 "${type_cond.class1}"
		#end if
	
		variableMetadata_out "$variableMetadata_out"
		graphs_out "$graphs_out"
	</command>

	<inputs>
		<param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
		<param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
		<param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
		
		<param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
	
		<conditional name="type_cond">
			<param name="type" type="select" label="Type" display="radio" help="Which class do you want to test ?">
				<option value="One_class">Tests between one class and the remaining samples </option>
				<option value="Each_class">Tests for each class </option>
			</param>
			<when value="One_class">
				<param name="class1" type="text" label="Selected class" help="This class is the numerator for the fold test" />
			</when>
			<when value="Each_class">
			</when>
		</conditional>
		
	</inputs>
	
	<outputs>
		<data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
		<data name="graphs_out" label="IC_Graphs" format="pdf" />
	</outputs>
	
	<help>

.. class:: infomark

**Authors** 
  | Anthony Fernandes - PFEM ; INRA 

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

========================
Intensity Check
========================

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

This tool performs two tests: the fold calculation, the number and the proportion of missing values. 

**Fold:**
The test calculates the ratio between two classes.
In the column name, the first class specified is the one used like numerator for the ratio.

**Missing values:**
This tool calculates the number and the proportion of missing values considering the class. 
Missing values in numerical columns of data must be coded NA.

**Two types of tests:**
	|	- Between **one class** and the remaining samples: if you have only two classes or if you want to test only one class.
	|	- **Each class**: if the column class contains at least three classes and you want to test each of them.

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

+----------------------------+------------+
| Parameter                  |   Format   |
+============================+============+
| 1 : Data Matrix file       |   tabular  |
+----------------------------+------------+
| 2 : Sample metadata file   |   tabular  |
+----------------------------+------------+
| 3 : Variable metadata file |   tabular  |
+----------------------------+------------+

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

**Class column**
	| Select the class column in Sample metadata.

**Type**
	|  Two options:
	|     - "One class" allows to perform tests on one class against the remaining samples.
	|     - "Each class" allows to add several columns with the ratio and the number of missing values for each class.

**Selected class**
	| If the type is "one class", specify it to calculate the ratio and the number of missing values. 

------------
Output file
------------

**Variable metadata file**
	| Contains the previous columns in variable metadata and the new ones with fold tests, numbers and proportion of missing values.
	
**Graphs file**
	| Contains barplots with the proportion of NA considering classes and boxplots with the folds values

	</help>
	
	
</tool>