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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
author peterjc
date Fri, 09 Nov 2018 11:15:23 -0500
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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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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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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. (2014). 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)"; P. Birch, J. Jones, and J.I. Bos, eds.
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58 Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7.
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59 http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7
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60
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61 For the associated RXLR Galaxy tool, please cite:
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62
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63 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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64 Galaxy tools and workflows for sequence analysis with applications
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65 in molecular plant pathology. PeerJ 1:e167
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66 https://doi.org/10.7717/peerj.167
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67
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68 For the three underlying methods, please cite:
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69
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70 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
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71 A translocation signal for delivery of oomycete effector proteins into
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72 host plant cells. Nature 450:115-118.
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73 https://doi.org/10.1038/nature06203
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74
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75 Win, J., Morgan, W., Bos, J., et al. (2007)
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76 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
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77 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
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78 https://doi.org/10.1105/tpc.107.051037
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79
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80 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
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81 The malarial host-targeting signal is conserved in the Irish potato famine
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82 pathogen. PLoS Pathogens 2(5):e50.
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83 https://doi.org/10.1371/journal.ppat.0020050
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86 Dependencies
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87 ============
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88
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89 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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90
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91 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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92 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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93 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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94
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95 However, at the time of writing those Galaxy tools have their own dependencies
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96 required for this workflow which require manual installation (SignalP v3.0,
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97 HMMER v2.0, and the R/Bioconductor package limma).
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100 History
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101 =======
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102
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103 ======= ======================================================================
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104 Version Changes
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105 ------- ----------------------------------------------------------------------
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106 v0.0.1 - Initial release to Tool Shed (May, 2013)
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107 - Expanded README file to include example data
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108 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
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109 tool to avoid warning about new ``header_lines`` parameter.
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110 - Added link to Tool Shed in the workflow annotation explaining there
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111 is a README file with sample data, and a requested citation.
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112 - Bundle sample output image for display in this README file.
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113 v0.0.3 - Use MIT licence.
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114 ======= ======================================================================
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116
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117 Developers
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118 ==========
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119
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120 This workflow is under source code control here:
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121
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122 https://github.com/peterjc/pico_galaxy/tree/master/workflows/rxlr_venn_workflow
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124 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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125
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126 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png
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128 Check this,
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129
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130 $ tar -tzf rxlr_venn_workflow.tar.gz
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131 README.rst
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132 repository_dependencies.xml
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133 rxlr_venn_workflow.ga
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134 Phyca11_example_output.png
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135
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136
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137 Licence (MIT)
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138 =============
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139
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140 Permission is hereby granted, free of charge, to any person obtaining a copy
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141 of this software and associated documentation files (the "Software"), to deal
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142 in the Software without restriction, including without limitation the rights
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143 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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144 copies of the Software, and to permit persons to whom the Software is
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145 furnished to do so, subject to the following conditions:
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146
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147 The above copyright notice and this permission notice shall be included in
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148 all copies or substantial portions of the Software.
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149
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150 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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151 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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152 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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153 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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154 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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155 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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156 THE SOFTWARE.