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author peterjc
date Fri, 25 Oct 2013 10:20:46 -0400
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1 This is package is a Galaxy workflow for comparing three RXLR prediction 1 This is package is a Galaxy workflow for comparing three RXLR prediction
2 methods with a Venn Diagram, and creates a FASTA file of any proteins 2 methods with a Venn Diagram, and creates a FASTA file of any proteins
3 passing all three methods. 3 passing all three methods.
4 4
5 See http://www.galaxyproject.org for information about the Galaxy Project. 5 See http://www.galaxyproject.org for information about the Galaxy Project.
6
7
8 Sample Data
9 ===========
10
11 This workflow was developed and run on several Phytophthora species.
12 For example, try the "Phyca11" protein set for Phytophthora capsici:
13
14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
15
16 You can upload this directly into Galaxy via this URL. Galaxy will handle
17 removing the gzip compression to give you the FASTA protein file which
18 has 19,805 protein sequences. The expected results:
19
20 * 89 RXLRs using Whisson et al. (2007)
21 * 124 RXLRs using Win et al. (2007)
22 * 162 RXLRs using Bhattacharjee et al. (2006)
23
24 Of these, only 79 sequences pass all three of the RXLR prediction tools,
25 while 19643 have no RXLR matches at all.
26
27 .. image:: https://raw.github.com/peterjc/picobio/master/galaxy_workflows/rxlr_venn_workflow/Phyca11_example_output.png
28 :height: 400px
29 :width: 400px
30
31
32 Citation
33 ========
34
35 If you use this workflow directly, or a derivative of it, in work leading
36 to a scientific publication, please cite:
37
38 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
39 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
40 Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
41 Humana Press, Springer. In press.
42
43 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
44 A translocation signal for delivery of oomycete effector proteins into
45 host plant cells. Nature 450:115-118.
46 http://dx.doi.org/10.1038/nature06203
47
48 Win, J., Morgan, W., Bos, J., et al. (2007)
49 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
50 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
51 http://dx.doi.org/10.1105/tpc.107.051037
52
53 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
54 The malarial host-targeting signal is conserved in the Irish potato famine
55 pathogen. PLoS Pathogens 2(5):e50.
56 http://dx.doi.org/10.1371/journal.ppat.0020050
57 6
58 7
59 Availability 8 Availability
60 ============ 9 ============
61 10
68 17
69 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow 18 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
70 19
71 Development is being done on github here: 20 Development is being done on github here:
72 21
73 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow 22 https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow
23
24
25 Sample Data
26 ===========
27
28 This workflow was developed and run on several *Phytophthora* species.
29 For example, try the "Phyca11" protein set for *Phytophthora capsici*:
30
31 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
32
33 You can upload this directly into Galaxy via this URL. Galaxy will handle
34 removing the gzip compression to give you the FASTA protein file which
35 has 19,805 protein sequences. The expected results:
36
37 * 89 RXLRs using Whisson et al. (2007)
38 * 124 RXLRs using Win et al. (2007)
39 * 162 RXLRs using Bhattacharjee et al. (2006)
40
41 Of these, only 79 sequences pass all three of the RXLR prediction tools,
42 while 19643 have no RXLR matches at all.
43
44 .. image:: Phyca11_example_output.png
45 :height: 400px
46 :width: 400px
47
48
49 Citation
50 ========
51
52 If you use this workflow directly, or a derivative of it, in work leading
53 to a scientific publication, please cite:
54
55 Cock, P.J.A. and Pritchard, L. (2014). Galaxy as a platform for identifying
56 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
57 Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds.
58 Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7.
59 http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7
60
61 For the associated RXLR Galaxy tool, please cite:
62
63 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
64 Galaxy tools and workflows for sequence analysis with applications
65 in molecular plant pathology. PeerJ 1:e167
66 http://dx.doi.org/10.7717/peerj.167
67
68 For the three underlying methods, please cite:
69
70 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
71 A translocation signal for delivery of oomycete effector proteins into
72 host plant cells. Nature 450:115-118.
73 http://dx.doi.org/10.1038/nature06203
74
75 Win, J., Morgan, W., Bos, J., et al. (2007)
76 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
77 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
78 http://dx.doi.org/10.1105/tpc.107.051037
79
80 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
81 The malarial host-targeting signal is conserved in the Irish potato famine
82 pathogen. PLoS Pathogens 2(5):e50.
83 http://dx.doi.org/10.1371/journal.ppat.0020050
74 84
75 85
76 Dependencies 86 Dependencies
77 ============ 87 ============
78 88
97 - Expanded README file to include example data 107 - Expanded README file to include example data
98 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter 108 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
99 tool to avoid warning about new ``header_lines`` parameter. 109 tool to avoid warning about new ``header_lines`` parameter.
100 - Added link to Tool Shed in the workflow annotation explaining there 110 - Added link to Tool Shed in the workflow annotation explaining there
101 is a README file with sample data, and a requested citation. 111 is a README file with sample data, and a requested citation.
112 - Bundle sample output image for display in this README file.
102 ======= ====================================================================== 113 ======= ======================================================================
103 114
104 115
105 Developers 116 Developers
106 ========== 117 ==========
107 118
108 This workflow is under source code control here: 119 This workflow is under source code control here:
109 120
110 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow 121 https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow
111 122
112 To prepare the tar-ball for uploading to the Tool Shed, I use this: 123 To prepare the tar-ball for uploading to the Tool Shed, I use this:
113 124
114 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga 125 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png
115 126
116 Check this, 127 Check this,
117 128
118 $ tar -tzf rxlr_venn_workflow.tar.gz 129 $ tar -tzf rxlr_venn_workflow.tar.gz
119 README.rst 130 README.rst
120 repository_dependencies.xml 131 repository_dependencies.xml
121 rxlr_venn_workflow.ga 132 rxlr_venn_workflow.ga
133 Phyca11_example_output.png