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

Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub

--- a/tools/protein_analysis/signalp3.xml	Thu Apr 25 12:25:52 2013 -0400
+++ b/tools/protein_analysis/signalp3.xml	Wed Sep 18 06:16:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="signalp3" name="SignalP 3.0" version="0.0.11">
+<tool id="signalp3" name="SignalP 3.0" version="0.0.12">
     <description>Find signal peptides in protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
@@ -7,7 +7,8 @@
       signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file
       ##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 defaults to one.
+      ##If the environment variable isn't set, get "", and the python wrapper
+      ##defaults to four threads.
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -167,23 +168,33 @@
 
 **References**
 
-Bendtsen, Nielsen, von Heijne, and Brunak.
+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
+
+Bendtsen, Nielsen, von Heijne, and Brunak (2004).
 Improved prediction of signal peptides: SignalP 3.0.
-J. Mol. Biol., 340:783-795, 2004.
+J. Mol. Biol., 340:783-795.
 http://dx.doi.org/10.1016/j.jmb.2004.05.028
 
-Nielsen, Engelbrecht, Brunak and von Heijne.
+Nielsen, Engelbrecht, Brunak and von Heijne (1997).
 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
-Protein Engineering, 10:1-6, 1997.
+Protein Engineering, 10:1-6.
 http://dx.doi.org/10.1093/protein/10.1.1
 
-Nielsen and Krogh.
+Nielsen and Krogh (1998).
 Prediction of signal peptides and signal anchors by a hidden Markov model.
 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6),
-AAAI Press, Menlo Park, California, pp. 122-130, 1998.
+AAAI Press, Menlo Park, California, pp. 122-130.
 http://www.ncbi.nlm.nih.gov/pubmed/9783217
 
-http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
+See also http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
 
+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>