Mercurial > repos > peterjc > seq_rename
changeset 8:0965642b1d14 draft
Uploaded v0.0.4d, citation information
| author | peterjc |
|---|---|
| date | Wed, 11 Sep 2013 06:39:12 -0400 |
| parents | e440681dd17c |
| children | 5a1b7d0d9f27 |
| files | tools/filters/repository_dependencies.xml tools/filters/seq_rename.py tools/filters/seq_rename.rst tools/filters/seq_rename.xml |
| diffstat | 4 files changed, 17 insertions(+), 9 deletions(-) [+] |
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--- 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>
--- 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):
--- 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). ======= ======================================================================
--- 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.