# HG changeset patch # User peterjc # Date 1380899865 14400 # Node ID 120d01a025a97e9777d5717f3cf9fa41c4bde0a2 # Parent 923fa257756453ba2547e57bb68304158f0738d4 Uploaded v0.0.2a, bundle sample image for display in README.rst (no functional changes) diff -r 923fa2577564 -r 120d01a025a9 Phyca11_example_output.png Binary file Phyca11_example_output.png has changed diff -r 923fa2577564 -r 120d01a025a9 README.rst --- a/README.rst Wed Aug 21 13:00:43 2013 -0400 +++ b/README.rst Fri Oct 04 11:17:45 2013 -0400 @@ -5,57 +5,6 @@ See http://www.galaxyproject.org for information about the Galaxy Project. -Sample Data -=========== - -This workflow was developed and run on several Phytophthora species. -For example, try the "Phyca11" protein set for Phytophthora capsici: - -http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz - -You can upload this directly into Galaxy via this URL. Galaxy will handle -removing the gzip compression to give you the FASTA protein file which -has 19,805 protein sequences. The expected results: - -* 89 RXLRs using Whisson et al. (2007) -* 124 RXLRs using Win et al. (2007) -* 162 RXLRs using Bhattacharjee et al. (2006) - -Of these, only 79 sequences pass all three of the RXLR prediction tools, -while 19643 have no RXLR matches at all. - -.. image:: https://raw.github.com/peterjc/picobio/master/galaxy_workflows/rxlr_venn_workflow/Phyca11_example_output.png - :height: 400px - :width: 400px - - -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 ============ @@ -70,7 +19,67 @@ Development is being done on github here: -https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow +https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow + + +Sample Data +=========== + +This workflow was developed and run on several *Phytophthora* species. +For example, try the "Phyca11" protein set for *Phytophthora capsici*: + +http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz + +You can upload this directly into Galaxy via this URL. Galaxy will handle +removing the gzip compression to give you the FASTA protein file which +has 19,805 protein sequences. The expected results: + +* 89 RXLRs using Whisson et al. (2007) +* 124 RXLRs using Win et al. (2007) +* 162 RXLRs using Bhattacharjee et al. (2006) + +Of these, only 79 sequences pass all three of the RXLR prediction tools, +while 19643 have no RXLR matches at all. + +.. image:: Phyca11_example_output.png + :height: 400px + :width: 400px + + +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. + +For the associated RXLR Galaxy tool, please cite: + +Peter J.A. Cock, Björn A. Grüning, 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 + +For the three underlying methods, please cite: + +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 Dependencies @@ -99,6 +108,7 @@ tool to avoid warning about new ``header_lines`` parameter. - Added link to Tool Shed in the workflow annotation explaining there is a README file with sample data, and a requested citation. + - Bundle sample output image for display in this README file. ======= ====================================================================== @@ -107,11 +117,11 @@ This workflow is under source code control here: -https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow +https://github.com/peterjc/pico_galaxy/tree/master/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 + $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png Check this, @@ -119,3 +129,4 @@ README.rst repository_dependencies.xml rxlr_venn_workflow.ga + Phyca11_example_output.png diff -r 923fa2577564 -r 120d01a025a9 repository_dependencies.xml --- a/repository_dependencies.xml Wed Aug 21 13:00:43 2013 -0400 +++ b/repository_dependencies.xml Fri Oct 04 11:17:45 2013 -0400 @@ -1,9 +1,9 @@ - + - + - +