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comparison tools/protein_analysis/signalp3.xml @ 16:7de64c8b258d draft

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Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:16:58 -0400
parents 99b82a2b1272
children e6cc27d182a8
comparison
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15:6abd809cefdd 16:7de64c8b258d
1 <tool id="signalp3" name="SignalP 3.0" version="0.0.11"> 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.12">
2 <description>Find signal peptides in protein sequences</description> 2 <description>Find signal peptides in protein sequences</description>
3 <!-- If job splitting is enabled, break up the query file into parts --> 3 <!-- If job splitting is enabled, break up the query file into parts -->
4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> 4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
6 <command interpreter="python"> 6 <command interpreter="python">
7 signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file 7 signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file
8 ##Set the number of threads in the runner entry in universe_wsgi.ini 8 ##Set the number of threads in the runner entry in universe_wsgi.ini
9 ##which (on SGE at least) will set the $NSLOTS environment variable. 9 ##which (on SGE at least) will set the $NSLOTS environment variable.
10 ##If the environment variable isn't set, get "", and defaults to one. 10 ##If the environment variable isn't set, get "", and the python wrapper
11 ##defaults to four threads.
11 </command> 12 </command>
12 <stdio> 13 <stdio>
13 <!-- Anything other than zero is an error --> 14 <!-- Anything other than zero is an error -->
14 <exit_code range="1:" /> 15 <exit_code range="1:" />
15 <exit_code range=":-1" /> 16 <exit_code range=":-1" />
165 166
166 Signal peptides are found at the start of a protein, so there is limited value in providing the full length sequence, and providing the full sequence slows down the analysis. Furthermore, SignalP has an upper bound on the sequence length it will accept (6000bp). Thus for practical reasons it is useful to truncate the proteins before passing them to SignalP. However, the precise point they are truncated does have a small influence on some score values, and thus to the results. 167 Signal peptides are found at the start of a protein, so there is limited value in providing the full length sequence, and providing the full sequence slows down the analysis. Furthermore, SignalP has an upper bound on the sequence length it will accept (6000bp). Thus for practical reasons it is useful to truncate the proteins before passing them to SignalP. However, the precise point they are truncated does have a small influence on some score values, and thus to the results.
167 168
168 **References** 169 **References**
169 170
170 Bendtsen, Nielsen, von Heijne, and Brunak. 171 If you use this Galaxy tool in work leading to a scientific publication please
172 cite the following papers:
173
174 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
175 Galaxy tools and workflows for sequence analysis with applications
176 in molecular plant pathology. PeerJ 1:e167
177 http://dx.doi.org/10.7717/peerj.167
178
179 Bendtsen, Nielsen, von Heijne, and Brunak (2004).
171 Improved prediction of signal peptides: SignalP 3.0. 180 Improved prediction of signal peptides: SignalP 3.0.
172 J. Mol. Biol., 340:783-795, 2004. 181 J. Mol. Biol., 340:783-795.
173 http://dx.doi.org/10.1016/j.jmb.2004.05.028 182 http://dx.doi.org/10.1016/j.jmb.2004.05.028
174 183
175 Nielsen, Engelbrecht, Brunak and von Heijne. 184 Nielsen, Engelbrecht, Brunak and von Heijne (1997).
176 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. 185 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
177 Protein Engineering, 10:1-6, 1997. 186 Protein Engineering, 10:1-6.
178 http://dx.doi.org/10.1093/protein/10.1.1 187 http://dx.doi.org/10.1093/protein/10.1.1
179 188
180 Nielsen and Krogh. 189 Nielsen and Krogh (1998).
181 Prediction of signal peptides and signal anchors by a hidden Markov model. 190 Prediction of signal peptides and signal anchors by a hidden Markov model.
182 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6), 191 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6),
183 AAAI Press, Menlo Park, California, pp. 122-130, 1998. 192 AAAI Press, Menlo Park, California, pp. 122-130.
184 http://www.ncbi.nlm.nih.gov/pubmed/9783217 193 http://www.ncbi.nlm.nih.gov/pubmed/9783217
185 194
186 http://www.cbs.dtu.dk/services/SignalP-3.0/output.php 195 See also http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
187 196
197 This wrapper is available to install into other Galaxy Instances via the Galaxy
198 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
188 </help> 199 </help>
189 </tool> 200 </tool>