# HG changeset patch
# User peterjc
# Date 1378895952 14400
# Node ID 0965642b1d147afa4de8f7857470dcb7c64e415f
# Parent  e440681dd17cf102e0526fa7ad103e596bca5b23
Uploaded v0.0.4d, citation information

diff -r e440681dd17c -r 0965642b1d14 tools/filters/repository_dependencies.xml
--- a/tools/filters/repository_dependencies.xml	Wed Jul 24 11:30:04 2013 -0400
+++ b/tools/filters/repository_dependencies.xml	Wed Sep 11 06:39:12 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>
diff -r e440681dd17c -r 0965642b1d14 tools/filters/seq_rename.py
--- a/tools/filters/seq_rename.py	Wed Jul 24 11:30:04 2013 -0400
+++ b/tools/filters/seq_rename.py	Wed Sep 11 06:39:12 2013 -0400
@@ -18,15 +18,15 @@
 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK.
-All rights reserved. See accompanying text file for licence details (MIT/BSD
-style).
+All rights reserved. See accompanying text file for licence details (MIT
+license).
 
-This is version 0.0.2 of the script.
+This is version 0.0.4 of the script.
 """
 import sys
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.2"
+    print "v0.0.4"
     sys.exit(0)
 
 def stop_err(msg, err=1):
diff -r e440681dd17c -r 0965642b1d14 tools/filters/seq_rename.rst
--- a/tools/filters/seq_rename.rst	Wed Jul 24 11:30:04 2013 -0400
+++ b/tools/filters/seq_rename.rst	Wed Sep 11 06:39:12 2013 -0400
@@ -68,6 +68,7 @@
 v0.0.4   - Automated installation of Biopython dependency.
          - Use reStructuredText for this README file.
          - Adopt standard MIT License.
+         - Updated citation information (Cock et al. 2013).
 ======= ======================================================================
 
 
diff -r e440681dd17c -r 0965642b1d14 tools/filters/seq_rename.xml
--- a/tools/filters/seq_rename.xml	Wed Jul 24 11:30:04 2013 -0400
+++ b/tools/filters/seq_rename.xml	Wed Sep 11 06:39:12 2013 -0400
@@ -61,11 +61,18 @@
 WARNING: If the tabular file has more than one new name for any old ID, the
 last one is used.
 
-**Citation**
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
 
-This tool uses Biopython to read and write SFF files. If you use this tool in
-scientific work leading to a publication, please cite the Biopython application
-note (and Galaxy too of course):
+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 to read and write SFF files, 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.