--- a/Marea/ras_generator.xml	Wed Feb 19 10:44:52 2020 -0500
+++ b/Marea/ras_generator.xml	Sun Feb 23 09:41:14 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.2">
+<tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.3">
     <description>- Reaction Activity Scores computation</description>
     <macros>
         <import>marea_macros.xml</import>
@@ -31,17 +31,6 @@
             </when>
             <when value="Custom">
                 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
-                <conditional name="cond_map">
-                    <param name="yes_no" type="select" label="Custom map? (optional)">
-                        <option value="no" selected="true">no</option>
-                        <option value="yes">yes</option>
-                    </param>
-                    <when value="yes">
-                        <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
-                    </when>
-                    <when value="no">
-                    </when>
-                </conditional>
             </when>
         </conditional>
         <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
@@ -59,6 +48,62 @@
 
 What it does
 -------------
+
+This tool computes Reaction Activity Scores from gene expression (RNA-seq) dataset(s), as described in Graudenzi et al. Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. Journal of Biomedical Informatics, 2018, 87: 37-49.
+ 
+Accepted files:
+    - A gene expression dataset
+ 
+Format:
+Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
+Column header: sample ID.
+Row header: gene ID.
+ 
+ 
+Optional files:
+    - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
+
+	* (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
+	* .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
+ 
+Computation option ‘(A and NaN) solved as (A)’:
+In case of missing expression value, referred to as NaN (Not a Number), for a gene joined with an AND operator in a given GPR rule, the rule ‘A and NaN’
+ 
+If YES is selected: the GPR will be solved as A.
+ 
+If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).
+
+Example input
+-------------
+
+Custom GPR rules:
+
++------------+--------------------------------------+   
+| id         |         rule (with entrez-id         |   
++============+======================================+   
+| r1642      |             155060 or 10357          |   
++------------+--------------------------------------+    
+| r1643      |        155060 or 100134869           |    
++------------+--------------------------------------+    
+| r1640      |     155060 and 100134869 or 10357    |   
++------------+--------------------------------------+
+
+RNA-seq dataset:
+
++------------+----------------+----------------+----------------+ 
+| Hugo_ID    |   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
++============+================+================+================+
+| HGNC:24086 |    0.523167    |    0.371355    |    0.925661    |  
++------------+----------------+----------------+----------------+    
+| HGNC:24086 |    0.568765    |    0.765567    |    0.456789    |    
++------------+----------------+----------------+----------------+    
+| HGNC:9876  |    0.876545    |    0.768933    |    0.987654    |  
++------------+----------------+----------------+----------------+
+| HGNC:9     |    0.456788    |    0.876543    |    0.876542    |    
++------------+----------------+----------------+----------------+    
+| HGNC:23    |    0.876543    |    0.786543    |    0.897654    |   
++------------+----------------+----------------+----------------+
+
 ]]>
     </help>
     <expand macro="citations" />