annotate Intchecks/xml_intensity_check.xml @ 1:4973a2104cfd draft

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<tool id="intens_check" name="Intensity Check" version="1.0.1">
	<description>Adding informations about intensities (mean fold change and missing values) 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}"
		fold_frac "${type_cond.fold_frac}"
		#end if
		
		logarithm "$logarithm"
	
		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="What kind of tests do you want to perform?" display="radio" help="If you only have two classes, 'One class' could be selected to choose which class should be on the numerator/denominator.">
				<option value="One_class">Tests between one class and the remaining samples </option>
				<option value="Each_class" selected="true">Tests for each class </option>
			</param>
			<when value="One_class">
				<param name="class1" type="text" label="Selected class" help="Class name if you choose to test one class against the remaining samples." />
				<param name="fold_frac" type="select" label="Where should the class be placed for the mean fold change calculation?" display="radio">
					<option value="Top">Numerator (Top) </option>
					<option value="Bottom">Denominator (Bottom) </option>
				</param>
			</when>
			<when value="Each_class">
			</when>
		</conditional>
		
		<param name="logarithm" type="select" label="Logarithm" help="Choose if you want the mean fold change to be converted into a log mean fold change (log2 or log10)">
			<option value="none">none </option>
			<option value="log2">log2 </option>
			<option value="log10">log10 </option>
		</param>
		
	</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: a mean fold change calculation and the number of missing values. 

**Fold:**
The test calculates the mean fold change between two classes. It could be converted into a logarithm.
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 in data matrix 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. Otherwise, you have two classes and you want to choose the one used like numerator or denominator for the mean fold change.

-----------
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 of test**
	|  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 between all the classes 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. 
	
**Numerator or denominator**
	| If the type is "one class", choose "top" or "bottom" to put the selected class as numerator or denominator (respectively) for the mean fold change.
	
**Logarithm**
	| Choose if you want to transform the mean fold change with a log2 or log10.

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

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

	</help>
	
	
</tool>