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diff sequel_wrapper.xml @ 2:208ce57f9221 draft default tip

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Fix version for blat requirement (reported by Bjoern Gruening). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation.
author crs4
date Fri, 18 Jul 2014 09:19:43 -0400
parents ccadfae70b02
children
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--- 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>