--- a/Intchecks/xml_intensity_check.xml	Fri Mar 08 09:07:12 2019 -0500
+++ b/Intchecks/xml_intensity_check.xml	Fri Jan 03 11:09:05 2020 -0500
@@ -1,7 +1,7 @@
-<tool id="intens_check" name="Intensity Check" version="1.2.1">
+<tool id="intens_check" name="Intensity Check" version="1.2.8">
 	<description>Statistical measures, number of missing values and mean fold change</description>
 	<requirements>
-	<requirement type="package" version="1.1_5">r-batch</requirement>
+	    <requirement type="package" version="1.1_5">r-batch</requirement>
 	</requirements>
 	<command interpreter="Rscript">
   
@@ -41,7 +41,7 @@
 	</command>
 
 	<inputs>
-		<param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
+		<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" />
 		
@@ -128,12 +128,15 @@
 		<data name="graphs_out" label="IC_Graphs" format="pdf" />
 	</outputs>
 	
+	
+	
 	<help>
 
 .. class:: infomark
 
-**Authors** 
-  | Anthony Fernandes - PFEM ; INRA 
+**Author:** 
+Anthony Fernandes for original code (PFEM - INRA) 
+**Maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB)
 
 ---------------------------------------------------
 
@@ -142,19 +145,39 @@
 ========================
 
 -----------
+Description
+-----------
+
+This tool performs various metrics: mean fold change calculation, number and proportion of missing values, and mean, sd and decile calculation.
+You can choose to perform these metrics according to sample groups defined in the sample metadata file given as input. 
+
+ 
+-----------------
+Workflow position
+-----------------
+
+
+.. image:: int_check.png
+        :width: 800
+
+
+-----------
 Input files
 -----------
 
 +----------------------------+------------+
 | Parameter                  |   Format   |
 +============================+============+
-| 1 : Data Matrix file       |   tabular  |
+| 1 : Data matrix file       |   tabular  |
 +----------------------------+------------+
 | 2 : Sample metadata file   |   tabular  |
 +----------------------------+------------+
 | 3 : Variable metadata file |   tabular  |
 +----------------------------+------------+
 
+	| 
+
+
 ----------
 Parameters
 ----------
@@ -167,21 +190,21 @@
 	| In the case of two classes: "each class" and "one class" give the same results for statistical measures. We recommend to choose "one class" for mean fold change calculation in order to select the class you want to put as numerator or denominator (see below).
 	
 **Statistics**
-	|  Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you could choose no statistical measure if you only want to calculate the mean fold change (see below).
+	|  Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you can choose to leave this section blank if you only want to calculate the mean fold change (see below).
 
-**Class column**
+**Class column** (*only if "each class" or "one class"*)
 	| Select the class column in sample metadata table.
 
-**Selected class**
+**Selected class** (*only if "one class"*)
 	| If the method is "one class", specify it. Remaining samples will be named "Other".
 	
-**Calculate the mean fold change**
+**Calculate the mean fold change** (*only if "each class" or "one class"*)
 	| Choose if you want to calculate the mean fold change. If the method is "each class": mean fold change will be calculated for all combinations of classes. If the method is "one class": it will be calculated between the selected class (see above) and the remaining samples.
 	
-**Where should the class be placed for the mean fold change calculation?**	
+**Where should the class be placed for the mean fold change calculation?** (*only if "one class"*)
 	| If the method is "one class", choose "top" or "bottom" to put the selected class as numerator or denominator (respectively) for the mean fold change calculation.	
 	
-**Logarithm**
+**Logarithm** (*only if "each class" or "one class"*)
 	| Choose if you want to transform the mean fold change with a log2 or log10.
 	
 ------------
@@ -190,11 +213,31 @@
 
 **Variable metadata file**
 	| Contains the previous columns in variable metadata file and the new ones.
-	| In the column names for fold, the first class specified is the one used like numerator for the ratio.
+	| In the column names for fold, the first class specified is the one used as numerator in the ratio.
 	
 **Graphs file**
 	| Contains barplots with the proportion of NA considering classes and boxplots with the fold values.
 
+
+
+---------------------------------------------------
+
+----------------------
+Additional information
+----------------------
+
+
+.. class:: warningmark
+
+For more information about input files, refer to the corresponding "W4M HowTo" page:
+ | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
+ |
+
+
+
+
+
+
 	</help>