# HG changeset patch # User peterjc # Date 1376926552 14400 # Node ID 1a1ab2f2b5b548959ffe068cbb1b45de46ebf11b # Parent fe5babf911e335f8c1bf1bb79683ac7eca2a592a README file with clearer citation instructions. diff -r fe5babf911e3 -r 1a1ab2f2b5b5 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Aug 19 11:35:52 2013 -0400 @@ -0,0 +1,82 @@ +This is package is a Galaxy workflow for comparing three RXLR prediction +methods with a Venn Diagram, and creates a FASTA file of any proteins +passing all three methods. + +See http://www.galaxyproject.org for information about the Galaxy Project. + + +Citation +======== + +If you use this workflow directly, or a derivative of it, in work leading +to a scientific publication, please cite: + +Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying +candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: +Methods and Protocols (Second Edition)"; Methods in Molecular Biology. +Humana Press, Springer. In press. + +Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007) +A translocation signal for delivery of oomycete effector proteins into +host plant cells. Nature 450:115-118. +http://dx.doi.org/10.1038/nature06203 + +Win, J., Morgan, W., Bos, J., et al. (2007) +Adaptive evolution has targeted the C-terminal domain of the RXLR effectors +of plant pathogenic oomycetes. The Plant Cell 19:2349-2369. +http://dx.doi.org/10.1105/tpc.107.051037 + +Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006) +The malarial host-targeting signal is conserved in the Irish potato famine +pathogen. PLoS Pathogens 2(5):e50. +http://dx.doi.org/10.1371/journal.ppat.0020050 + + +Availability +============ + +This workflow is available to download and/or install from the main +Galaxy Tool Shed: + +http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow + +Test releases (which should not normally be used) are on the Test Tool Shed: + +http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow + +Development is being done on github here: + +https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow + + +Dependencies +============ + +These dependencies should be resolved automatically via the Galaxy Tool Shed: + +* http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp +* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id +* http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list + +However, at the time of writing those Galaxy tools have their own dependencies +required for this workflow which require manual installation (SignalP v3.0, +HMMER v2.0, and the R/Bioconductor package limma). + + +Developers +========== + +This workflow is under source code control here: + +https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow + +To prepare the tar-ball for uploading to the Tool Shed, I use this: + + $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga + +Check this, + + $ tar -tzf rxlr_venn_workflow.tar.gz + README.rst + repository_dependencies.xml + rxlr_venn_workflow.ga diff -r fe5babf911e3 -r 1a1ab2f2b5b5 README.txt --- a/README.txt Tue May 07 13:53:56 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -This Tool Shed Repository contains a workflow for comparing three RXLR -prediction methods with a Venn Diagram, and creates a FASTA file of any -proteins passing all three methods. - - -References -========== - -Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, -Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, -Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard -and Paul R. J. Birch A translocation signal for delivery of oomycete -effector proteins into host plant cells. Nature 450:115-118, 2007. -http://dx.doi.org/10.1038/nature06203 - -Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, -Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun. -Adaptive evolution has targeted the C-terminal domain of the RXLR effectors -of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007. -http://dx.doi.org/10.1105/tpc.107.051037 - -Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, -Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar. -The malarial host-targeting signal is conserved in the Irish potato famine -pathogen. PLoS Pathogens, 2(5):e50, 2006. -http://dx.doi.org/10.1371/journal.ppat.0020050 - - -Availability -============ - -This workflow is available on the main Galaxy Tool Shed: -http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow - -Development is being done on github here: -https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow - - -Dependencies -============ - -These dependencies should be resolved automatically via the Galaxy Tool Shed: - * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp - * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id - * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list - -However, at the time of writing those Galaxy tools have their own dependencies -required for this workflow which require manual installation (SignalP v3.0, -HMMER v2.0, and the R/Bioconductor package limma). diff -r fe5babf911e3 -r 1a1ab2f2b5b5 repository_dependencies.xml --- a/repository_dependencies.xml Tue May 07 13:53:56 2013 -0400 +++ b/repository_dependencies.xml Mon Aug 19 11:35:52 2013 -0400 @@ -1,9 +1,9 @@ - + - - - + + +