# HG changeset patch
# User peterjc
# Date 1378894538 14400
# Node ID 66e15f0eefb14d392f36685ed5528c696c16239e
# Parent  2dedcbc5f4b6731e008cfdd408f5526a918ba592
Uploaded v0.0.5d, citation information

diff -r 2dedcbc5f4b6 -r 66e15f0eefb1 tools/filters/get_orfs_or_cdss.rst
--- a/tools/filters/get_orfs_or_cdss.rst	Wed Jul 24 11:31:54 2013 -0400
+++ b/tools/filters/get_orfs_or_cdss.rst	Wed Sep 11 06:15:38 2013 -0400
@@ -3,7 +3,7 @@
 
 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
+See the licence text below (MIT licence).
 
 This tool is a short Python script (using Biopython library functions)
 to search nucleotide sequences for open reading frames (ORFs) or coding
@@ -66,6 +66,7 @@
 v0.0.5   - Automated intallation of the Biopython dependency.
          - Use reStructuredText for this README file.
          - Adopt standard MIT License.
+         - Updated citation information (Cock et al. 2013).
 ======= ======================================================================
 
 
diff -r 2dedcbc5f4b6 -r 66e15f0eefb1 tools/filters/get_orfs_or_cdss.xml
--- a/tools/filters/get_orfs_or_cdss.xml	Wed Jul 24 11:31:54 2013 -0400
+++ b/tools/filters/get_orfs_or_cdss.xml	Wed Sep 11 06:15:38 2013 -0400
@@ -152,9 +152,16 @@
 
 **Citation**
 
-This tool uses Biopython. If you use this tool in scientific work leading
-to a publication, please cite the Biopython application note (and Galaxy
-too of course):
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following paper:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+This tool uses Biopython, so you may also wish to cite the Biopython
+application note (and Galaxy too of course):
 
 Cock et al 2009. Biopython: freely available Python tools for computational
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
diff -r 2dedcbc5f4b6 -r 66e15f0eefb1 tools/filters/repository_dependencies.xml
--- a/tools/filters/repository_dependencies.xml	Wed Jul 24 11:31:54 2013 -0400
+++ b/tools/filters/repository_dependencies.xml	Wed Sep 11 06:15:38 2013 -0400
@@ -2,5 +2,5 @@
 <repositories description="This requires Biopython as a dependency.">
 <!-- Leave out the tool shed and revision to get the current
      tool shed and latest revision at the time of upload -->
-<repository changeset_revision="627c7b41b970" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+<repository changeset_revision="54e5c64b0460" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>