--- a/viscorvar_networkvar.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/viscorvar_networkvar.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -20,17 +20,15 @@
 
         --output_graph ${output_graph}
 
-        @COMMAND_LOG_EXIT@
+    ]]></command>
 
-    ]]></command>
-   
     <inputs>
         <param name="mat_similarity_rdata" type="data" format="rdata"
                label="this is the RData output file from the computeMatSimilarity function"
-               help="output RData file from computeMatSimilarity"/>
+               help="output RData file from the computeMatSimilarity function"/>
         <param name="var_list_file" type="data" format="tabular"
                label="Variables list file"
-               help="selected variables output tabular file from circleCor"/>
+               help="selected variables output tabular file from the circleCor function"/>
 
         <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
         <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
@@ -39,7 +37,7 @@
 
         <param name="response_var_list" type="data" format="tabular"
                label="List of response variables"
-               help="output *_response_var.tsv file from matCorAddVar"/>
+               help="output *_response_var.tsv file from the matCorAddVar function"/>
         <param name="select_response_var" type="select" display="checkboxes" multiple="true"
                label="Response variables"
                help="response variables that will be plotted in the network">
@@ -72,10 +70,10 @@
 -----------
 
 This tool creates a network of correlated variables for omics datasets. The determination of
-the omics datasets which can be visualized is made by the tool matCorAddVar. This network can
+the omics datasets which can be visualized is made by the matCorAddVar tool. This network can
 be exported to graphml format and visualized with Cytoscape. The link between two variables
 is associated with the correlation between two variables : a threshold can be used in
-Cytoscape to get a network of variables whose correlation is greater than this threshold
+Cytoscape to get a network of variables whose correlations are greater than this threshold
 in absolute value.
 
 -----------------
@@ -105,9 +103,9 @@
 +===========================================================+===========+
 | 1 : Rdata visCorVar.computeMatSimilarity output           |  rdata    |
 +-----------------------------------------------------------+-----------+
-| 2 : ``*``_selected_var.tsv visCorVar.circleCor output     |  tabular  |
+| 2 : \*_selected_var.tsv visCorVar.circleCor output        |  tabular  |
 +-----------------------------------------------------------+-----------+
-| 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output  |  tabular  |
+| 3 : \*_response_var.tsv visCorVar.matCorAddVar output     |  tabular  |
 +-----------------------------------------------------------+-----------+
 
 ----------
@@ -127,4 +125,4 @@
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>