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author peterjc
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
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2 methods with a Venn Diagram, and creates a FASTA file of any proteins
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3 passing all three methods.
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5 See http://www.galaxyproject.org for information about the Galaxy Project.
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8 Availability
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9 ============
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11 This workflow is available to download and/or install from the main
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12 Galaxy Tool Shed:
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14 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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16 Test releases (which should not normally be used) are on the Test Tool Shed:
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18 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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20 Development is being done on github here:
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21
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22 https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow
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25 Sample Data
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26 ===========
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28 This workflow was developed and run on several *Phytophthora* species.
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29 For example, try the "Phyca11" protein set for *Phytophthora capsici*:
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31 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
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32
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33 You can upload this directly into Galaxy via this URL. Galaxy will handle
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34 removing the gzip compression to give you the FASTA protein file which
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35 has 19,805 protein sequences. The expected results:
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37 * 89 RXLRs using Whisson et al. (2007)
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38 * 124 RXLRs using Win et al. (2007)
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39 * 162 RXLRs using Bhattacharjee et al. (2006)
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41 Of these, only 79 sequences pass all three of the RXLR prediction tools,
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42 while 19643 have no RXLR matches at all.
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43
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44 .. image:: Phyca11_example_output.png
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45 :height: 400px
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46 :width: 400px
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49 Citation
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50 ========
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51
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52 If you use this workflow directly, or a derivative of it, in work leading
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53 to a scientific publication, please cite:
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54
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55 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
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56 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
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57 Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
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58 Humana Press, Springer. In press.
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59
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60 For the associated RXLR Galaxy tool, please cite:
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61
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62 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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63 Galaxy tools and workflows for sequence analysis with applications
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64 in molecular plant pathology. PeerJ 1:e167
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65 http://dx.doi.org/10.7717/peerj.167
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66
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67 For the three underlying methods, please cite:
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68
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69 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
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70 A translocation signal for delivery of oomycete effector proteins into
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71 host plant cells. Nature 450:115-118.
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72 http://dx.doi.org/10.1038/nature06203
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73
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74 Win, J., Morgan, W., Bos, J., et al. (2007)
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75 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
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76 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
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77 http://dx.doi.org/10.1105/tpc.107.051037
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78
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79 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
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80 The malarial host-targeting signal is conserved in the Irish potato famine
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81 pathogen. PLoS Pathogens 2(5):e50.
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82 http://dx.doi.org/10.1371/journal.ppat.0020050
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84
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85 Dependencies
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86 ============
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87
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88 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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89
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90 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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91 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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92 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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93
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94 However, at the time of writing those Galaxy tools have their own dependencies
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95 required for this workflow which require manual installation (SignalP v3.0,
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96 HMMER v2.0, and the R/Bioconductor package limma).
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98
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99 History
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100 =======
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101
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102 ======= ======================================================================
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103 Version Changes
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104 ------- ----------------------------------------------------------------------
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105 v0.0.1 - Initial release to Tool Shed (May, 2013)
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106 - Expanded README file to include example data
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107 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
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108 tool to avoid warning about new ``header_lines`` parameter.
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109 - Added link to Tool Shed in the workflow annotation explaining there
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110 is a README file with sample data, and a requested citation.
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111 - Bundle sample output image for display in this README file.
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112 ======= ======================================================================
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114
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115 Developers
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116 ==========
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117
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118 This workflow is under source code control here:
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119
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120 https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow
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122 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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123
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124 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png
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126 Check this,
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127
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128 $ tar -tzf rxlr_venn_workflow.tar.gz
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129 README.rst
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130 repository_dependencies.xml
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131 rxlr_venn_workflow.ga
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132 Phyca11_example_output.png