| Previous changeset 6:2dedcbc5f4b6 (2013-07-24) Next changeset 8:c673f3b291b2 (2013-09-12) |
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Commit message:
Uploaded v0.0.5d, citation information |
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modified:
tools/filters/get_orfs_or_cdss.rst tools/filters/get_orfs_or_cdss.xml tools/filters/repository_dependencies.xml |
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| 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 |
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| @@ -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). ======= ====================================================================== |
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| 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 |
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| @@ -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. |
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| 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 |
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| @@ -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> |