Mercurial > repos > peterjc > get_orfs_or_cdss
changeset 7:66e15f0eefb1 draft
Uploaded v0.0.5d, citation information
| author | peterjc |
|---|---|
| date | Wed, 11 Sep 2013 06:15:38 -0400 |
| parents | 2dedcbc5f4b6 |
| children | c673f3b291b2 |
| files | tools/filters/get_orfs_or_cdss.rst tools/filters/get_orfs_or_cdss.xml tools/filters/repository_dependencies.xml |
| diffstat | 3 files changed, 13 insertions(+), 5 deletions(-) [+] |
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--- 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). ======= ======================================================================
--- 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.
--- 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>