--- a/viscorvar_matcoraddvar.xml	Fri Oct 23 11:26:18 2020 +0000
+++ b/viscorvar_matcoraddvar.xml	Tue Nov 17 13:01:44 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
+<tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
 
     <description>determine the correlation circles that can be overlaid and compute the correlations</description>
 
@@ -34,14 +34,14 @@
     <inputs>
         <param name="input_rdata" type="data" format="rdata"
                label="Input RData file from block.SPLSDA"
-               help="This is the RData output file from the block.splsda function." />
+               help="this is the RData output file from the block.splsda function" />
         <param name="block_Y" type="data" format="tabular"
                label="Block Y"
-               help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
+               help="Block Y is a table. A column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). For the file structure, see below in the section Input files" />
         <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
         <param name="var_of_interest_file" type="data" format="txt" optional="true"
                label="Variables of interest (Optional)"
-               help="variables not belonging to any block will not be considered"/>
+               help="variables not belonging to any block will not be considered. For the file structure, see below in the section Input files"/>
         <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
                label="Cutoff comp"
                help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> -->
@@ -68,7 +68,12 @@
 Description
 -----------
 
-Bla bla...
+This tool is a pre-processing step of the pipeline. It computes the correlations
+between omics datasets variables, variables of interest (optional), response variables and
+the components which are output of the data integration. The variables of interest are omics
+datasets variables that will be added to the network. It also determines the omics datasets
+for which the correlated variables of these omics datasets can be visualized with correlation
+circles and networks.
 
 -----------------
 Workflow position
@@ -110,6 +115,15 @@
 | 3 : [opt] Variables of interest         |  txt      |
 +-----------------------------------------+-----------+
 
+2. Block Y structure
+Block Y is in tabular format (.tsv).
+This table contains the name of the samples in the first column.
+The other columns correspond to phenotypes.
+For each of these other columns, a column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). The names of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order.
+
+3. Variables of interest structure
+All the variables of interest are in the same column.
+
 ----------
 Parameters
 ----------