Mercurial > repos > peterjc > rxlr_venn_workflow
annotate README.rst @ 4:3c280e01b920 draft
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
| author | peterjc |
|---|---|
| date | Wed, 21 Aug 2013 13:01:51 -0400 |
| parents | 1a1ab2f2b5b5 |
| children | 4726b640f221 |
| rev | line source |
|---|---|
| 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 | |
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8 Sample Data |
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9 =========== |
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10 |
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11 This workflow was developed and run on several Phytophthora species. |
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12 For example, try the "Phyca11" protein set for Phytophthora capsici: |
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13 |
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14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz |
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15 |
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16 You can upload this directly into Galaxy via this URL. Galaxy will handle |
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17 removing the gzip compression to give you the FASTA protein file which |
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18 has 19,805 protein sequences. The expected results: |
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19 |
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20 * 89 RXLRs using Whisson et al. (2007) |
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21 * 124 RXLRs using Win et al. (2007) |
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22 * 162 RXLRs using Bhattacharjee et al. (2006) |
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23 |
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24 Of these, only 79 sequences pass all three of the RXLR prediction tools, |
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25 while 19643 have no RXLR matches at all. |
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26 |
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27 .. image:: https://raw.github.com/peterjc/picobio/master/galaxy_workflows/rxlr_venn_workflow/Phyca11_example_output.png |
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28 :height: 400px |
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29 :width: 400px |
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30 |
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31 |
| 3 | 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 | |
| 58 | |
| 59 Availability | |
| 60 ============ | |
| 61 | |
| 62 This workflow is available to download and/or install from the main | |
| 63 Galaxy Tool Shed: | |
| 64 | |
| 65 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow | |
| 66 | |
| 67 Test releases (which should not normally be used) are on the Test Tool Shed: | |
| 68 | |
| 69 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow | |
| 70 | |
| 71 Development is being done on github here: | |
| 72 | |
| 73 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow | |
| 74 | |
| 75 | |
| 76 Dependencies | |
| 77 ============ | |
| 78 | |
| 79 These dependencies should be resolved automatically via the Galaxy Tool Shed: | |
| 80 | |
| 81 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp | |
| 82 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
| 83 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list | |
| 84 | |
| 85 However, at the time of writing those Galaxy tools have their own dependencies | |
| 86 required for this workflow which require manual installation (SignalP v3.0, | |
| 87 HMMER v2.0, and the R/Bioconductor package limma). | |
| 88 | |
| 89 | |
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90 History |
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91 ======= |
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92 |
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93 ======= ====================================================================== |
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94 Version Changes |
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95 ------- ---------------------------------------------------------------------- |
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96 v0.0.1 - Initial release to Tool Shed (May, 2013) |
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97 - Expanded README file to include example data |
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98 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter |
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99 tool to avoid warning about new ``header_lines`` parameter. |
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100 - Added link to Tool Shed in the workflow annotation explaining there |
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101 is a README file with sample data, and a requested citation. |
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102 ======= ====================================================================== |
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103 |
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104 |
| 3 | 105 Developers |
| 106 ========== | |
| 107 | |
| 108 This workflow is under source code control here: | |
| 109 | |
| 110 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow | |
| 111 | |
| 112 To prepare the tar-ball for uploading to the Tool Shed, I use this: | |
| 113 | |
| 114 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga | |
| 115 | |
| 116 Check this, | |
| 117 | |
| 118 $ tar -tzf rxlr_venn_workflow.tar.gz | |
| 119 README.rst | |
| 120 repository_dependencies.xml | |
| 121 rxlr_venn_workflow.ga |