Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/psortb.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
equal deleted inserted replaced
15:6abd809cefdd 16:7de64c8b258d
1 <tool id="Psortb" name="psortb" version="0.0.1"> 1 <tool id="Psortb" name="psortb" version="0.0.3">
2 <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description> 2 <description>Determines sub-cellular localisation of bacterial/archaeal 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 <version_command interpreter="python">psortb.py --version</version_command> 6 <version_command interpreter="python">psortb.py --version</version_command>
7 <command interpreter="python">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command> 7 <command interpreter="python">
8 psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
9 ##I want the number of threads to be a Galaxy config option...
10 ##Set the number of threads in the runner entry in universe_wsgi.ini
11 ##which (on SGE at least) will set the $NSLOTS environment variable.
12 ##If the environment variable isn't set, get "", and python wrapper
13 ##defaults to four threads.
14 </command>
8 <stdio> 15 <stdio>
9 <!-- Anything other than zero is an error --> 16 <!-- Anything other than zero is an error -->
10 <exit_code range="1:" /> 17 <exit_code range="1:" />
11 <exit_code range=":-1" /> 18 <exit_code range=":-1" />
12 </stdio> 19 </stdio>
74 so that Galaxy treats it as a comment) giving the column names. 81 so that Galaxy treats it as a comment) giving the column names.
75 82
76 83
77 **References** 84 **References**
78 85
86 If you use this Galaxy tool in work leading to a scientific publication please
87 cite the following papers:
88
89 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
90 Galaxy tools and workflows for sequence analysis with applications
91 in molecular plant pathology. PeerJ 1:e167
92 http://dx.doi.org/10.7717/peerj.167
93
79 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, 94 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
80 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010) 95 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
81 PSORTb 3.0: Improved protein subcellular localization prediction with 96 PSORTb 3.0: Improved protein subcellular localization prediction with
82 refined localization subcategories and predictive capabilities for all 97 refined localization subcategories and predictive capabilities for all
83 prokaryotes, Bioinformatics 26(13):1608-1615 98 prokaryotes, Bioinformatics 26(13):1608-1615
84 http://dx.doi.org/10.1093/bioinformatics/btq249 99 http://dx.doi.org/10.1093/bioinformatics/btq249
85 100
86 http://www.psort.org/documentation/index.html 101 See also http://www.psort.org/documentation/index.html
87 102
103 This wrapper is available to install into other Galaxy Instances via the Galaxy
104 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
88 </help> 105 </help>
89 </tool> 106 </tool>