Mercurial > repos > peterjc > rxlr_venn_workflow
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author | peterjc |
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date | Fri, 04 Oct 2013 11:17:45 -0400 |
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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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4 |
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5 See http://www.galaxyproject.org for information about the Galaxy Project. |
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6 |
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7 |
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8 Availability |
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9 ============ |
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10 |
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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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13 |
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14 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow |
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15 |
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16 Test releases (which should not normally be used) are on the Test Tool Shed: |
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17 |
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18 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow |
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19 |
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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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23 |
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24 |
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25 Sample Data |
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26 =========== |
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27 |
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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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30 |
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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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36 |
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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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40 |
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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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47 |
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48 |
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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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83 |
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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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97 |
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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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113 |
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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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121 |
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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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125 |
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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 |