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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 13:00:43 -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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5 See http://www.galaxyproject.org for information about the Galaxy Project.
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8 Sample Data
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9 ===========
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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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14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
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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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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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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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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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32 Citation
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33 ========
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35 If you use this workflow directly, or a derivative of it, in work leading
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36 to a scientific publication, please cite:
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38 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
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39 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
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40 Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
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41 Humana Press, Springer. In press.
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43 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
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44 A translocation signal for delivery of oomycete effector proteins into
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45 host plant cells. Nature 450:115-118.
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46 http://dx.doi.org/10.1038/nature06203
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48 Win, J., Morgan, W., Bos, J., et al. (2007)
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49 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
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50 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
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51 http://dx.doi.org/10.1105/tpc.107.051037
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53 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
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54 The malarial host-targeting signal is conserved in the Irish potato famine
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55 pathogen. PLoS Pathogens 2(5):e50.
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56 http://dx.doi.org/10.1371/journal.ppat.0020050
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59 Availability
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60 ============
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61
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62 This workflow is available to download and/or install from the main
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63 Galaxy Tool Shed:
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65 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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67 Test releases (which should not normally be used) are on the Test Tool Shed:
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68
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69 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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71 Development is being done on github here:
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73 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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76 Dependencies
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77 ============
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78
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79 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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81 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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82 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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83 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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84
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85 However, at the time of writing those Galaxy tools have their own dependencies
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86 required for this workflow which require manual installation (SignalP v3.0,
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87 HMMER v2.0, and the R/Bioconductor package limma).
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90 History
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91 =======
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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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105 Developers
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106 ==========
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107
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108 This workflow is under source code control here:
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109
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110 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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111
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112 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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113
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114 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga
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115
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116 Check this,
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117
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118 $ tar -tzf rxlr_venn_workflow.tar.gz
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119 README.rst
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120 repository_dependencies.xml
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121 rxlr_venn_workflow.ga