changeset 353:978a883ab2f4 draft

Uploaded

--- a/marea_2/flux_to_map.xml	Thu Aug 29 20:24:59 2024 +0000
+++ b/marea_2/flux_to_map.xml	Thu Aug 29 20:31:50 2024 +0000
@@ -144,17 +144,17 @@
 What it does
 -------------
 
-This tool analyzes and visualizes differences in reactions fluxes of groups of samples, returned by the Flux Simulation tool, of groups of samples.
+This tool analyzes and visualizes differences in reactions fluxes of groups of samples returned by the Flux Simulation tool.
 
 Accepted files are: 
     - option 1) two or more fluxes datasets, each referring to samples in a given group. The user can specify a label for each group;
     - option 2) one fluxes dataset and one group-file specifying the group each sample belongs to (e.g. the accepted group file is thought to be the one returned by the Clustering tool).
 
 Optional files:
-    - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
+    - custom svg map. Graphical elements must have the same IDs of reactions.
 
 The tool generates:
-    - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
+    - 1) a tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes;
     - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
     - 3) a log file (.txt).
     
@@ -170,12 +170,12 @@
 Example input
 -------------
 
-"RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
+"Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N" option:
 
-RAS Dataset 1:
+Fluxes Dataset 1:
 
 +------------+----------------+----------------+----------------+ 
-| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
+| Reaction ID|   Patient1     |   Patient2     |   Patient3     |  
 +============+================+================+================+
 | r1642      |    0.523167    |    0.371355    |    0.925661    |  
 +------------+----------------+----------------+----------------+    
@@ -188,10 +188,10 @@
 | r1646      |    0.876543    |    0.786543    |    0.897654    |   
 +------------+----------------+----------------+----------------+
 
-RAS Dataset 2:
+Fluxes Dataset 2:
 
 +------------+----------------+----------------+----------------+ 
-| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
+| Reaction ID|   Patient1     |   Patient2     |   Patient3     |  
 +============+================+================+================+
 | r1642      |    0.523167    |    0.371355    |    0.925661    |  
 +------------+----------------+----------------+----------------+    
@@ -204,12 +204,12 @@
 | r1646      |    0.876543    |    0.786543    |    0.897654    |   
 +------------+----------------+----------------+----------------+
 
-"RAS of all samples + sample group specification" option:
+"Fluxes of all samples + sample group specification" option:
 
-RAS Dataset:
+Fluxes Dataset:
 
 +------------+----------------+----------------+----------------+ 
-| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
+| Reaction ID|   Patient1     |   Patient2     |   Patient3     |  
 +============+================+================+================+
 | r1642      |    0.523167    |    0.371355    |    0.925661    |  
 +------------+----------------+----------------+----------------+    
@@ -227,11 +227,11 @@
 +---------------+-----------+
 | Patient ID    |   Class   | 
 +===============+===========+
-| TCGAAA3529    |    MSI    | 
+| Patient1      |    0      | 
 +---------------+-----------+  
-| TCGAA62671    |    MSS    |    
+| Patient2      |    1      |    
 +---------------+-----------+   
-| TCGAA62672    |    MSI    |
+| Patient3      |    1      |
 +---------------+-----------+
 
 
@@ -239,8 +239,6 @@
 
 .. class:: infomark
 
-**TIP**: This tool using the RAS scores computed by `Ras tool`_.
-
 ]]>
 	</help>
 	<expand macro="citations" />