--- a/viscorvar_matcoraddvar.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/viscorvar_matcoraddvar.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -27,8 +27,6 @@
         --output_response_var ${output_response_var}
         --output_blocks_comb ${output_blocks_comb}
 
-        @COMMAND_LOG_EXIT@
-
     ]]></command>
 
     <inputs>
@@ -37,7 +35,7 @@
                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 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" />
+               help="Block Y is a table. A column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 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)"
@@ -119,7 +117,7 @@
 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.
+For each of these other columns, a column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 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.
@@ -135,16 +133,14 @@
 ------------
 
 viscorvar_matcoraddvar_output.RData
-    RData output
-
-viscorvar_matcoraddvar_response_var.tsv
-
+    | RData output
+    | Contains the `matCorAddVar_result` R object containing the result of the matCorAddVar function
 
 viscorvar_matcoraddvar_blocks_comb.tsv
-
+    | viscorvar_matcoraddvar_blocks_comb.tsv contains the block names whose correlation circles can be overlaid
 
     ]]></help>
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>