Mercurial > repos > crs4 > edge_pro

diff edge_pro.xml @ 3:ddcbf8732706 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
author crs4
date Mon, 19 Jan 2015 12:48:51 -0500
parents bad8a51514dd
children d5464c9e1723
line wrap: on
line diff
--- a/edge_pro.xml	Wed Mar 05 06:44:35 2014 -0500
+++ b/edge_pro.xml	Mon Jan 19 12:48:51 2015 -0500
@@ -112,19 +112,22 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: http://opensource.org/licenses/MIT
 
-If you use this tool in Galaxy, please cite |Cuccuru2013|_.
-
-.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
-.. _Cuccuru2013: http://orione.crs4.it/
-
-This tool uses `EDGE-pro`_, which is licensed separately. Please cite |Magoc2013|_.
+You can use this tool only if you agree to the license terms of: `EDGE-pro`_.
 
 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Magoc2013|_.
+
+.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
 .. |Magoc2013| replace:: Magoc, T., Wood, D., Salzberg, S. L. (2013) EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. *Evol. Bioinform.* 2013:9, 127-136
 .. _Magoc2013: http://www.la-press.com/edge-pro-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586
   </help>