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

--- 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>