Mercurial > repos > peterjc > rxlr_venn_workflow
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| author | peterjc |
|---|---|
| date | Fri, 25 Oct 2013 10:20:46 -0400 |
| parents | 3c280e01b920 |
| children |
| rev | line source |
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| 3 | 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 | |
| 3 passing all three methods. | |
| 4 | |
| 5 See http://www.galaxyproject.org for information about the Galaxy Project. | |
| 6 | |
| 7 | |
| 8 Availability | |
| 9 ============ | |
| 10 | |
| 11 This workflow is available to download and/or install from the main | |
| 12 Galaxy Tool Shed: | |
| 13 | |
| 14 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow | |
| 15 | |
| 16 Test releases (which should not normally be used) are on the Test Tool Shed: | |
| 17 | |
| 18 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow | |
| 19 | |
| 20 Development is being done on github here: | |
| 21 | |
| 5 | 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 | |
| 3 | 84 |
| 85 | |
| 86 Dependencies | |
| 87 ============ | |
| 88 | |
| 89 These dependencies should be resolved automatically via the Galaxy Tool Shed: | |
| 90 | |
| 91 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp | |
| 92 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
| 93 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list | |
| 94 | |
| 95 However, at the time of writing those Galaxy tools have their own dependencies | |
| 96 required for this workflow which require manual installation (SignalP v3.0, | |
| 97 HMMER v2.0, and the R/Bioconductor package limma). | |
| 98 | |
| 99 | |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
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100 History |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
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101 ======= |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
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changeset
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102 |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
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changeset
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103 ======= ====================================================================== |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
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diff
changeset
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104 Version Changes |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
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105 ------- ---------------------------------------------------------------------- |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
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106 v0.0.1 - Initial release to Tool Shed (May, 2013) |
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3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
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107 - Expanded README file to include example data |
|
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
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108 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter |
|
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
|
109 tool to avoid warning about new ``header_lines`` parameter. |
|
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
|
110 - Added link to Tool Shed in the workflow annotation explaining there |
|
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
|
111 is a README file with sample data, and a requested citation. |
| 5 | 112 - Bundle sample output image for display in this README file. |
|
4
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
|
113 ======= ====================================================================== |
|
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
|
114 |
|
3c280e01b920
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
peterjc
parents:
3
diff
changeset
|
115 |
| 3 | 116 Developers |
| 117 ========== | |
| 118 | |
| 119 This workflow is under source code control here: | |
| 120 | |
| 5 | 121 https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow |
| 3 | 122 |
| 123 To prepare the tar-ball for uploading to the Tool Shed, I use this: | |
| 124 | |
| 5 | 125 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png |
| 3 | 126 |
| 127 Check this, | |
| 128 | |
| 129 $ tar -tzf rxlr_venn_workflow.tar.gz | |
| 130 README.rst | |
| 131 repository_dependencies.xml | |
| 132 rxlr_venn_workflow.ga | |
| 5 | 133 Phyca11_example_output.png |