Mercurial > repos > peterjc > secreted_protein_workflow
annotate README.rst @ 2:3a0c0d1c388f draft
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
| author | peterjc |
|---|---|
| date | Wed, 21 Aug 2013 11:58:54 -0400 |
| parents | 606da4e1d925 |
| children | 72f03c2102ee |
| rev | line source |
|---|---|
| 1 | 1 This is package is a Galaxy workflow for the identification of candidate |
| 2 secreted proteins from a given protein FASTA file. | |
| 3 | |
| 4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a | |
| 5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001) | |
| 6 on those, and selects only proteins without a predicted trans-membrane helix. | |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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7 This workflow was used in Kikuchi et al. (2011), and is a simplification of |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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8 the candidate effector protocol described in Jones et al. (2009). |
| 1 | 9 |
| 10 See http://www.galaxyproject.org for information about the Galaxy Project. | |
| 11 | |
| 12 | |
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13 Sample Data |
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14 =========== |
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15 |
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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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16 This workflow was developed and run on several nematode species. For example, |
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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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17 try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011): |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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18 |
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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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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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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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20 |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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21 You can upload this directly into Galaxy via this URL. Galaxy will handle |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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22 removing the gzip compression to give you the FASTA protein file which has |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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23 18,074 sequences. The expected result (selecting organism type Eukaryote) |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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24 is a FASTA protein file of 2,297 predicted secreted protein sequences. |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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25 |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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26 |
| 1 | 27 Citation |
| 28 ======== | |
| 29 | |
| 30 If you use this workflow directly, or a derivative of it, in work leading | |
| 31 to a scientific publication, please cite: | |
| 32 | |
| 33 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying | |
| 34 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: | |
| 35 Methods and Protocols (Second Edition)"; Methods in Molecular Biology. | |
| 36 Humana Press, Springer. In press. | |
| 37 | |
| 38 Also consider citing: | |
| 39 | |
| 40 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004) | |
| 41 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95. | |
| 42 http://dx.doi.org/10.1016/j.jmb.2004.05.028 | |
| 43 | |
| 44 Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001) | |
| 45 Predicting transmembrane protein topology with a hidden Markov model: | |
| 46 application to complete genomes. J Mol Biol 305: 567- 580. | |
| 47 http://dx.doi.org/10.1006/jmbi.2000.4315 | |
| 48 | |
| 49 | |
| 50 Additional References | |
| 51 ===================== | |
| 52 | |
| 53 Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011) | |
| 54 Genomic insights into the origin of parasitism in the emerging plant | |
| 55 pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219. | |
| 56 http://dx.doi.org/10.1371/journal.ppat.1002219 | |
| 57 | |
| 58 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009) | |
| 59 Identification and functional characterization of effectors in expressed | |
| 60 sequence tags from various life cycle stages of the potato cyst nematode | |
| 61 Globodera pallida. Mol Plant Pathol 10: 815–28. | |
| 62 http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x | |
| 63 | |
| 64 | |
| 65 Availability | |
| 66 ============ | |
| 67 | |
| 68 This workflow is available to download and/or install from the main | |
| 69 Galaxy Tool Shed: | |
| 70 | |
| 71 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow | |
| 72 | |
| 73 Test releases (which should not normally be used) are on the Test Tool Shed: | |
| 74 | |
| 75 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow | |
| 76 | |
| 77 Development is being done on github here: | |
| 78 | |
| 79 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow | |
| 80 | |
| 81 | |
| 82 Dependencies | |
| 83 ============ | |
| 84 | |
| 85 These dependencies should be resolved automatically via the Galaxy Tool Shed: | |
| 86 | |
| 87 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp | |
| 88 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
| 89 | |
| 90 However, at the time of writing those Galaxy tools have their own | |
| 91 dependencies required for this workflow which require manual | |
| 92 installation (SignalP v3.0 and TMHMM v2.0). | |
| 93 | |
| 94 | |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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95 History |
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peterjc
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96 ======= |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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97 |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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98 ======= ====================================================================== |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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99 Version Changes |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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100 ------- ---------------------------------------------------------------------- |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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101 v0.0.1 - Initial release to Tool Shed (May, 2013) |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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102 - Expanded README file to include example data |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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103 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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104 tool to avoid warning about new ``header_lines`` parameter. |
|
3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
parents:
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105 ======= ====================================================================== |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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106 |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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107 |
| 1 | 108 Developers |
| 109 ========== | |
| 110 | |
| 111 This workflow is under source code control here: | |
| 112 | |
| 113 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow | |
| 114 | |
| 115 To prepare the tar-ball for uploading to the Tool Shed, I use this: | |
| 116 | |
| 117 $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga | |
| 118 | |
| 119 Check this, | |
| 120 | |
| 121 $ tar -tzf secreted_protein_workflow.tar.gz | |
| 122 README.rst | |
| 123 repository_dependencies.xml | |
| 124 secreted_protein_workflow.ga |