Mercurial > repos > peterjc > secreted_protein_workflow
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
author | peterjc |
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date | Fri, 09 Nov 2018 11:16:44 -0500 |
parents | cb25a70933ea |
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This is package is a Galaxy workflow for the identification of candidate secreted proteins from a given protein FASTA file. It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001) on those, and selects only proteins without a predicted trans-membrane helix. This workflow was used in Kikuchi et al. (2011), and is a simplification of the candidate effector protocol described in Jones et al. (2009). See http://www.galaxyproject.org for information about the Galaxy Project. Availability ============ This workflow is available to download and/or install from the main Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow Test releases (which should not normally be used) are on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow Development is being done on github here: https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow Sample Data =========== This workflow was developed and run on several nematode species. For example, try the protein set for *Bursaphelenchus xylophilus* (Kikuchi et al. 2011): ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz You can upload this directly into Galaxy via this URL. Galaxy will handle removing the gzip compression to give you the FASTA protein file which has 18,074 sequences. The expected result (selecting organism type Eukaryote) is a FASTA protein file of 2,297 predicted secreted protein sequences. Citation ======== If you use this workflow directly, or a derivative of it, in work leading to a scientific publication, please cite: Cock, P.J.A. and Pritchard, L. (2014). Galaxy as a platform for identifying candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds. Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7. http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 https://doi.org/10.7717/peerj.167 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95. https://doi.org/10.1016/j.jmb.2004.05.028 Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567- 580. https://doi.org/10.1006/jmbi.2000.4315 Additional References ===================== Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen *Bursaphelenchus xylophilus*. PLoS Pathog 7: e1002219. https://doi.org/10.1371/journal.ppat.1002219 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009) Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode *Globodera pallida*. Mol Plant Pathol 10: 815–28. https://doi.org/10.1111/j.1364-3703.2009.00585.x Dependencies ============ These dependencies should be resolved automatically via the Galaxy Tool Shed: * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id However, at the time of writing those Galaxy tools have their own dependencies required for this workflow which require manual installation (SignalP v3.0 and TMHMM v2.0). History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial release to Tool Shed (May, 2013) - Expanded README file to include example data v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter tool to avoid warning about new ``header_lines`` parameter. - Added link to Tool Shed in the workflow annotation explaining there is a README file with sample data, and a requested citation. v0.0.3 - Use MIT licence. ======= ====================================================================== Developers ========== This workflow is under source code control here: https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow To prepare the tar-ball for uploading to the Tool Shed, I use this: $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga Check this, $ tar -tzf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga Licence (MIT) ============= Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.