# HG changeset patch
# User bimib
# Date 1591193988 14400
# Node ID c22ba05473701ddddea6a1a492f135d68a50bee3
# Parent  19d704e249778933fa3a41f46bb989eb4bd868be
update links and pubblications.

diff -r 19d704e24977 -r c22ba0547370 Marea/local/HMRcoreMap.svg
diff -r 19d704e24977 -r c22ba0547370 Marea/local/HMRcore_genes.p
diff -r 19d704e24977 -r c22ba0547370 Marea/local/HMRcore_rules.p
diff -r 19d704e24977 -r c22ba0547370 Marea/local/Recon_genes.p
diff -r 19d704e24977 -r c22ba0547370 Marea/local/Recon_rules.p
diff -r 19d704e24977 -r c22ba0547370 Marea/local/desktop.ini
diff -r 19d704e24977 -r c22ba0547370 Marea/marea.py
diff -r 19d704e24977 -r c22ba0547370 Marea/marea.xml
--- a/Marea/marea.xml	Thu Apr 23 17:17:41 2020 -0400
+++ b/Marea/marea.xml	Wed Jun 03 10:19:48 2020 -0400
@@ -277,13 +277,18 @@
 
 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
 
+.. class:: infomark
+
+**TIP**: This tool using the RAS scores computed by `Ras tool`_.
+
 @REFERENCE@
 
-.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
-.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
-.. _MaREA cluster analysis: http://link del tool di cluster.org
+.. _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" />undefined</tool>
+<expand macro="citations" />
+</tool>
 	
diff -r 19d704e24977 -r c22ba0547370 Marea/marea_cluster.py
diff -r 19d704e24977 -r c22ba0547370 Marea/marea_cluster.xml
--- a/Marea/marea_cluster.xml	Thu Apr 23 17:17:41 2020 -0400
+++ b/Marea/marea_cluster.xml	Wed Jun 03 10:19:48 2020 -0400
@@ -132,8 +132,7 @@
     
 .. class:: infomark
 
-**TIP**: This tool has been conceived to cluster gene expression data, by using the RAS scores computed by the tool
-`MaREA`_ as feature
+**TIP**: This tool has been conceived to cluster gene expression data, by using the RAS scores computed by `Ras tool`_.
 
 .. class:: infomark
 
@@ -143,8 +142,8 @@
 
 @REFERENCE@
 
-.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
-.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
+.. _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
 
 
 ]]>
diff -r 19d704e24977 -r c22ba0547370 Marea/marea_macros.xml
--- a/Marea/marea_macros.xml	Thu Apr 23 17:17:41 2020 -0400
+++ b/Marea/marea_macros.xml	Wed Jun 03 10:19:48 2020 -0400
@@ -68,7 +68,7 @@
 
 This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_.
 
-.. _BIMIB: http://sito di bio.org
+.. _BIMIB: https://bimib.disco.unimib.it/index.php/Home
 .. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English
 .. _University of Milan - Bicocca: https://www.unimib.it/
 
@@ -77,14 +77,28 @@
     <xml name="citations">
         <citations> <!--esempio di citazione-->
             <citation type="bibtex">
-@online{lh32017,
-  author = {Alex Graudenzi, Davide Maspero, Cluadio Isella, Marzia Di Filippo, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani},
-  year = {2018},
-  title = {MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq},
-  publisher = {bioRxiv},
-  journal = {bioRxiv},
-  url = {https://www.biorxiv.org/content/early/2018/01/16/248724},
-}
+              @article{graudenzi2018integration,
+              title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power},
+              author={Graudenzi, Alex and Maspero, Davide and Di Filippo, Marzia and Gnugnoli, Marco and Isella, Claudio and Mauri, Giancarlo and Medico, Enzo and Antoniotti, Marco and Damiani, Chiara},
+              journal={Journal of biomedical informatics},
+              volume={87},
+              pages={37--49},
+              year={2018},
+              publisher={Elsevier},
+              url = {https://doi-org.proxy.unimib.it/10.1016/j.jbi.2018.09.010},
+              }
+            </citation>
+            <citation type="bibtex">
+              @article{damiani2020marea4galaxy,
+              title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy},
+              author={Damiani, Chiara and Rovida, Lorenzo and Maspero, Davide and Sala, Irene and Rosato, Luca and Di Filippo, Marzia and Pescini, Dario and Graudenzi, Alex and Antoniotti, Marco and Mauri, Giancarlo},
+              journal={Computational and Structural Biotechnology Journal},
+              volume={18},
+              pages={993},
+              year={2020},
+              publisher={Research Network of Computational and Structural Biotechnology},
+              url = {https://dx-doi-org.proxy.unimib.it/10.1016%2Fj.csbj.2020.04.008},
+              }
             </citation>
         </citations>
     </xml>
diff -r 19d704e24977 -r c22ba0547370 Marea/ras_generator.py
diff -r 19d704e24977 -r c22ba0547370 Marea/ras_generator.xml