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Uploaded v0.0.2, update tool versions (should fix filter warning)
author peterjc
date Wed, 21 Aug 2013 11:19:27 -0400
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1 This is package is a Galaxy workflow for the identification of candidate
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2 secreted proteins from a given protein FASTA file.
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4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
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5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
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6 on those, and selects only proteins without a predicted trans-membrane helix.
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7 This workflow was used in Kikuchi et al. (2011), and is a simplification of
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8 the candidate effector protocol described in Jones et al. (2009).
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10 See http://www.galaxyproject.org for information about the Galaxy Project.
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13 Sample Data
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14 ===========
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16 This workflow was developed and run on several nematode species. For example,
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17 try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011):
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19 ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz
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21 You can upload this directly into Galaxy via this URL. Galaxy will handle
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22 removing the gzip compression to give you the FASTA protein file which has
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23 18,074 sequences. The expected result (selecting organism type Eukaryote)
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24 is a FASTA protein file of 2,297 predicted secreted protein sequences.
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27 Citation
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28 ========
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29
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30 If you use this workflow directly, or a derivative of it, in work leading
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31 to a scientific publication, please cite:
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33 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
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34 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
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35 Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
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36 Humana Press, Springer. In press.
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38 Also consider citing:
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39
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40 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
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41 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
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42 http://dx.doi.org/10.1016/j.jmb.2004.05.028
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44 Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001)
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45 Predicting transmembrane protein topology with a hidden Markov model:
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46 application to complete genomes. J Mol Biol 305: 567- 580.
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47 http://dx.doi.org/10.1006/jmbi.2000.4315
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50 Additional References
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51 =====================
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52
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53 Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011)
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54 Genomic insights into the origin of parasitism in the emerging plant
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55 pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219.
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56 http://dx.doi.org/10.1371/journal.ppat.1002219
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57
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58 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)
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59 Identification and functional characterization of effectors in expressed
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60 sequence tags from various life cycle stages of the potato cyst nematode
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61 Globodera pallida. Mol Plant Pathol 10: 815–28.
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62 http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x
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65 Availability
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66 ============
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67
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68 This workflow is available to download and/or install from the main
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69 Galaxy Tool Shed:
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70
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71 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
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73 Test releases (which should not normally be used) are on the Test Tool Shed:
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75 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
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76
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77 Development is being done on github here:
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79 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
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82 Dependencies
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83 ============
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84
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85 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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86
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87 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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88 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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89
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90 However, at the time of writing those Galaxy tools have their own
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91 dependencies required for this workflow which require manual
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92 installation (SignalP v3.0 and TMHMM v2.0).
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95 History
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96 =======
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97
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98 ======= ======================================================================
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99 Version Changes
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100 ------- ----------------------------------------------------------------------
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101 v0.0.1 - Initial release to Tool Shed (May, 2013)
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102 - Expanded README file to include example data
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103 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
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104 tool to avoid warning about new ``header_lines`` parameter.
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105 ======= ======================================================================
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106
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107
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108 Developers
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109 ==========
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110
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111 This workflow is under source code control here:
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112
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113 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
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115 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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116
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117 $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga
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119 Check this,
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120
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121 $ tar -tzf secreted_protein_workflow.tar.gz
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122 README.rst
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123 repository_dependencies.xml
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124 secreted_protein_workflow.ga