Mercurial > repos > peterjc > rxlr_venn_workflow
comparison README.rst @ 13:120d01a025a9 draft
Uploaded v0.0.2a, bundle sample image for display in README.rst (no functional changes)
author | peterjc |
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date | Fri, 04 Oct 2013 11:17:45 -0400 |
parents | 923fa2577564 |
children | 25076bddafe8 |
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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. 2013. Galaxy as a platform for identifying | |
56 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: | |
57 Methods and Protocols (Second Edition)"; Methods in Molecular Biology. | |
58 Humana Press, Springer. In press. | |
59 | |
60 For the associated RXLR Galaxy tool, please cite: | |
61 | |
62 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
63 Galaxy tools and workflows for sequence analysis with applications | |
64 in molecular plant pathology. PeerJ 1:e167 | |
65 http://dx.doi.org/10.7717/peerj.167 | |
66 | |
67 For the three underlying methods, please cite: | |
68 | |
69 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007) | |
70 A translocation signal for delivery of oomycete effector proteins into | |
71 host plant cells. Nature 450:115-118. | |
72 http://dx.doi.org/10.1038/nature06203 | |
73 | |
74 Win, J., Morgan, W., Bos, J., et al. (2007) | |
75 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors | |
76 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369. | |
77 http://dx.doi.org/10.1105/tpc.107.051037 | |
78 | |
79 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006) | |
80 The malarial host-targeting signal is conserved in the Irish potato famine | |
81 pathogen. PLoS Pathogens 2(5):e50. | |
82 http://dx.doi.org/10.1371/journal.ppat.0020050 | |
74 | 83 |
75 | 84 |
76 Dependencies | 85 Dependencies |
77 ============ | 86 ============ |
78 | 87 |
97 - Expanded README file to include example data | 106 - Expanded README file to include example data |
98 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter | 107 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter |
99 tool to avoid warning about new ``header_lines`` parameter. | 108 tool to avoid warning about new ``header_lines`` parameter. |
100 - Added link to Tool Shed in the workflow annotation explaining there | 109 - Added link to Tool Shed in the workflow annotation explaining there |
101 is a README file with sample data, and a requested citation. | 110 is a README file with sample data, and a requested citation. |
111 - Bundle sample output image for display in this README file. | |
102 ======= ====================================================================== | 112 ======= ====================================================================== |
103 | 113 |
104 | 114 |
105 Developers | 115 Developers |
106 ========== | 116 ========== |
107 | 117 |
108 This workflow is under source code control here: | 118 This workflow is under source code control here: |
109 | 119 |
110 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow | 120 https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow |
111 | 121 |
112 To prepare the tar-ball for uploading to the Tool Shed, I use this: | 122 To prepare the tar-ball for uploading to the Tool Shed, I use this: |
113 | 123 |
114 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga | 124 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png |
115 | 125 |
116 Check this, | 126 Check this, |
117 | 127 |
118 $ tar -tzf rxlr_venn_workflow.tar.gz | 128 $ tar -tzf rxlr_venn_workflow.tar.gz |
119 README.rst | 129 README.rst |
120 repository_dependencies.xml | 130 repository_dependencies.xml |
121 rxlr_venn_workflow.ga | 131 rxlr_venn_workflow.ga |
132 Phyca11_example_output.png |