# HG changeset patch # User peterjc # Date 1382710846 14400 # Node ID 4726b640f221da805c51d0ed9e190d4268beeb8e # Parent 3c280e01b9202ffc59c40ecd5429641affe4e162 Uploaded revision to update the citation diff -r 3c280e01b920 -r 4726b640f221 Phyca11_example_output.png Binary file Phyca11_example_output.png has changed diff -r 3c280e01b920 -r 4726b640f221 README.rst --- a/README.rst Wed Aug 21 13:01:51 2013 -0400 +++ b/README.rst Fri Oct 25 10:20:46 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 +19,68 @@ 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. (2014). Galaxy as a platform for identifying +candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: +Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds. +Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7. +http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7 + +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 +109,7 @@ 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 +118,11 @@ 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 +130,4 @@ README.rst repository_dependencies.xml rxlr_venn_workflow.ga + Phyca11_example_output.png diff -r 3c280e01b920 -r 4726b640f221 repository_dependencies.xml --- a/repository_dependencies.xml Wed Aug 21 13:01:51 2013 -0400 +++ b/repository_dependencies.xml Fri Oct 25 10:20:46 2013 -0400 @@ -1,9 +1,9 @@ - + - + - + diff -r 3c280e01b920 -r 4726b640f221 rxlr_venn_workflow.ga --- a/rxlr_venn_workflow.ga Wed Aug 21 13:01:51 2013 -0400 +++ b/rxlr_venn_workflow.ga Fri Oct 25 10:20:46 2013 -0400 @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.
\n
\nThis workflow is available on the Galaxy Tool Shed with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2013).", + "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.
\n
\nThis workflow is available on the Galaxy Tool Shed with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2014).", "format-version": "0.1", "name": "3 RXLR methods, Venn Diagram, overlap FASTA", "steps": {