# HG changeset patch
# User crs4
# Date 1405689583 14400
# Node ID 208ce57f9221c2a393918102eb32eadbef81434f
# Parent  ccadfae70b02fb41aa5ce5e4e09502c1e7efe5d7
Fix version for blat requirement (reported by Bjoern Gruening). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation.

diff -r ccadfae70b02 -r 208ce57f9221 readme.rst
--- a/readme.rst	Wed Mar 05 06:48:08 2014 -0500
+++ b/readme.rst	Fri Jul 18 09:19:43 2014 -0400
@@ -19,6 +19,7 @@
 Version history
 ---------------
 
+- Release 2: Fix version for blat requirement (reported by Björn Grüning). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation.
 - Release 1: Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
 - Release 0: Initial release in the Tool Shed.
 
diff -r ccadfae70b02 -r 208ce57f9221 sequel_wrapper.xml
--- a/sequel_wrapper.xml	Wed Mar 05 06:48:08 2014 -0500
+++ b/sequel_wrapper.xml	Fri Jul 18 09:19:43 2014 -0400
@@ -1,8 +1,8 @@
 <tool id="sequel_wrapper" name="SEQuel" version="0.2">
   <description></description>
   <requirements>
-    <requirement type="package" version="0.6.2">bwa</requirement>
-    <requirement type="package" version="35">blat</requirement>
+    <requirement type="package" version="0.7.7">bwa</requirement>
+    <requirement type="package" version="35x1">blat</requirement>
     <requirement type="package" version="1.0.2">sequel</requirement>
   </requirements>
   <command interpreter="python">
@@ -112,19 +112,22 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2013-2014 `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 `SEQuel`_, which is licensed separately. Please cite |Ronen2012|_.
+You can use this tool only if you agree to the license terms of: `SEQuel`_.
 
 .. _SEQuel: http://bix.ucsd.edu/SEQuel/
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Ronen2012|_.
+
+.. |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
 .. |Ronen2012| replace:: Ronen R., *et al.* (2012) SEQuel: improving the accuracy of genome assemblies. *Bioinformatics* 28 (12), i188-i196
 .. _Ronen2012: http://bioinformatics.oxfordjournals.org/content/28/12/i188
   </help>
diff -r ccadfae70b02 -r 208ce57f9221 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 05 06:48:08 2014 -0500
+++ b/tool_dependencies.xml	Fri Jul 18 09:19:43 2014 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="bwa" version="0.6.2">
-    <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <package name="bwa" version="0.7.7">
+    <repository changeset_revision="def70e393020" name="package_bwa_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="blat" version="35">
+  <package name="blat" version="35x1">
     <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="sequel" version="1.0.2">