Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/wolf_psort.xml @ 16:7de64c8b258d draft
Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
author | peterjc |
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date | Wed, 18 Sep 2013 06:16:58 -0400 |
parents | 6365217cd3de |
children | e6cc27d182a8 |
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--- a/tools/protein_analysis/wolf_psort.xml Thu Apr 25 12:25:52 2013 -0400 +++ b/tools/protein_analysis/wolf_psort.xml Wed Sep 18 06:16:58 2013 -0400 @@ -1,8 +1,12 @@ -<tool id="wolf_psort" name="WoLF PSORT" version="0.0.4"> +<tool id="wolf_psort" name="WoLF PSORT" version="0.0.6"> <description>Eukaryote protein subcellular localization prediction</description> <command interpreter="python"> - wolf_psort.py $organism 8 $fasta_file $tabular_file + wolf_psort.py $organism "\$NSLOTS" "$fasta_file" "$tabular_file" ##I want the number of threads to be a Galaxy config option... + ##Set the number of threads in the runner entry in universe_wsgi.ini + ##which (on SGE at least) will set the $NSLOTS environment variable. + ##If the environment variable isn't set, get "", and python wrapper + ##defaults to four threads. </command> <stdio> <!-- Anything other than zero is an error --> @@ -84,6 +88,11 @@ vacu vacuolar membrane 0005774(2) ====== ===================== ===================== +Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of" +cellular components were also included, up to the specified depth (2 in this case). +For example, all of the children and grandchildren of "GO:0005856" were +included as "cysk". + Additionally compound predictions like mito_nucl are also given. @@ -119,16 +128,26 @@ **References** -Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai, +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +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 +http://dx.doi.org/10.7717/peerj.167 + +Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai (2007). WoLF PSORT: Protein Localization Predictor. -Nucleic Acids Research, 35(S2), W585-W587, 2007. +Nucleic Acids Research, 35(S2), W585-W587. http://dx.doi.org/10.1093/nar/gkm259 -Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai. +Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai (2006). Protein Subcellular Localization Prediction with WoLF PSORT. -Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006. +Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48. -http://wolfpsort.org +See also http://wolfpsort.org +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp </help> </tool>