changeset 343:d2b382c86f0c draft

Uploaded

--- a/marea_2/flux_to_map.xml	Thu Aug 29 19:40:53 2024 +0000
+++ b/marea_2/flux_to_map.xml	Thu Aug 29 19:41:04 2024 +0000
@@ -144,16 +144,11 @@
 What it does
 -------------
 
-This tool analyzes and visualizes differences in the Reaction Activity Scores (RASs) of groups of samples, as computed by the Expression2RAS tool, of groups of samples.
+This tool analyzes and visualizes differences in reactions fluxes of groups of samples, returned by the Flux Simulation tool, of groups of samples.
 
 Accepted files are: 
-    - option 1) two or more RAS datasets, each referring to samples in a given group. The user can specify a label for each group (as e.g. "classA" and "classB");
-    - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
-    
-RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
-
-Column header: sample ID.
-Row header: reaction ID. 
+    - 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.
@@ -239,19 +234,6 @@
 | TCGAA62672    |    MSI    |
 +---------------+-----------+
 
-Advanced options
-----------------
-
-P-Value threshold: the threshold used for significance Kolmogorov-Smirnov (KS) test, to verify whether the distributions of RASs over the samples in two sets are significantly different
-
-Fold-Change threshold: threshold of the fold-change between the average RAS of two groups. Among the reactions that pass the KS test, only fold-change values larger than the indicated threshold will be visualized on the output metabolic map;
-
-
-.. class:: infomark
-
-**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
-
-.. class:: infomark
 
 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
 
@@ -259,12 +241,6 @@
 
 **TIP**: This tool using the RAS scores computed by `Ras tool`_.
 
-@REFERENCE@
-
-.. _Ras tool: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA+RAS+Generator%2F1.0.6&version=1.0.6&__identifer=auulv6gbp76
-.. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6
-.. _MaREA cluster analysis: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA_cluester%2F1.1.2&version=1.1.2&__identifer=lxbyzn2me9
-
 ]]>
 	</help>
 	<expand macro="citations" />