comparison Intchecks/xml_intensity_check.xml @ 2:a7553caa2572 draft

Uploaded

1:4973a2104cfd

<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">
  

-----------

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
-----------

----------
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.

------------
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>	

2:a7553caa2572

<tool id="intens_check" name="Intensity Check" version="1.0.1">
	<description>Adding information about intensities (mean fold change and missing values) in the variable metadata table</description>
	<requirements>
	<requirement type="package" version="1.1_4">r-batch</requirement>
	</requirements>
	<command interpreter="Rscript">
  

-----------

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 logarithm.

**Missing values:**
This tool calculates the number and the proportion of missing values in the 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 versus all the remaining samples without class distinction. 
	|	- **Each class**: if the class columns contains at least three classes and you want to test each of them. Can also be used with only two classes, but you will not choose which class to put as numerator/denominator. 

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

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

**Class column**
	| Select the class column in sample metadata table.

**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.

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

**Variable metadata file**
	| Contains the previous columns in variable metadata file and the new ones with fold tests, number and proportion of missing values.
	| In the column names for fold, the first class specified is the one used like numerator for the ratio.
	
**Graphs file**
	| Contains barplots with the proportion of NA considering classes and boxplots with the fold values.

	</help>
	
	
</tool>