Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/tmhmm2.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 dc958c2a963a
children e6cc27d182a8
comparison
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15:6abd809cefdd 16:7de64c8b258d
1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.10"> 1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.11">
2 <description>Find transmembrane domains in protein sequences</description> 2 <description>Find transmembrane domains 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 tmhmm2.py "\$NSLOTS" $fasta_file $tabular_file 7 tmhmm2.py "\$NSLOTS" $fasta_file $tabular_file
8 ##I want the number of threads to be a Galaxy config option...
8 ##Set the number of threads in the runner entry in universe_wsgi.ini 9 ##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. 10 ##which (on SGE at least) will set the $NSLOTS environment variable.
10 ##If the environment variable isn't set, get "", and defaults to one. 11 ##If the environment variable isn't set, get "", and the python wrapper
12 ##defaults to four threads.
11 </command> 13 </command>
12 <stdio> 14 <stdio>
13 <!-- Anything other than zero is an error --> 15 <!-- Anything other than zero is an error -->
14 <exit_code range="1:" /> 16 <exit_code range="1:" />
15 <exit_code range=":-1" /> 17 <exit_code range=":-1" />
92 94
93 ----- 95 -----
94 96
95 **References** 97 **References**
96 98
97 Krogh, Larsson, von Heijne, and Sonnhammer. 99 If you use this Galaxy tool in work leading to a scientific publication please
100 cite the following papers:
101
102 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
103 Galaxy tools and workflows for sequence analysis with applications
104 in molecular plant pathology. PeerJ 1:e167
105 http://dx.doi.org/10.7717/peerj.167
106
107 Krogh, Larsson, von Heijne, and Sonnhammer (2001).
98 Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. 108 Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes.
99 J. Mol. Biol. 305:567-580, 2001. 109 J. Mol. Biol. 305:567-580.
100 http://dx.doi.org/10.1006/jmbi.2000.4315 110 http://dx.doi.org/10.1006/jmbi.2000.4315
101 111
102 Sonnhammer, von Heijne, and Krogh. 112 Sonnhammer, von Heijne, and Krogh (1998).
103 A hidden Markov model for predicting transmembrane helices in protein sequences. 113 A hidden Markov model for predicting transmembrane helices in protein sequences.
104 In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press, 1998. 114 In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press.
105 http://www.ncbi.nlm.nih.gov/pubmed/9783223 115 http://www.ncbi.nlm.nih.gov/pubmed/9783223
106 116
107 http://www.cbs.dtu.dk/services/TMHMM/ 117 See also http://www.cbs.dtu.dk/services/TMHMM/
108 118
119 This wrapper is available to install into other Galaxy Instances via the Galaxy
120 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
109 </help> 121 </help>
110 </tool> 122 </tool>