Mercurial > repos > peterjc > rxlr_venn_workflow
annotate README.rst @ 15:00388d97c6e2 draft
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author | peterjc |
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date | Wed, 01 Feb 2017 13:20:54 -0500 |
parents | 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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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 |
14 | 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: |
14 | 57 Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds. |
58 Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7. | |
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 http://dx.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 http://dx.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 http://dx.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 http://dx.doi.org/10.1371/journal.ppat.0020050 |
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84 |
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85 |
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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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98 |
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99 |
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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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115 |
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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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123 |
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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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127 |
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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. |