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

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

--- a/tools/protein_analysis/psortb.xml	Thu Apr 25 12:25:52 2013 -0400
+++ b/tools/protein_analysis/psortb.xml	Wed Sep 18 06:16:58 2013 -0400
@@ -1,10 +1,17 @@
-<tool id="Psortb" name="psortb" version="0.0.1">
+<tool id="Psortb" name="psortb" version="0.0.3">
   <description>Determines sub-cellular localisation of bacterial/archaeal 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 -->
   <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
   <version_command interpreter="python">psortb.py --version</version_command>
-  <command interpreter="python">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command>
+  <command interpreter="python">
+    psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
+    ##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 -->
     <exit_code range="1:" />
@@ -76,6 +83,14 @@
 
 **References**
 
+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
+
 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
 PSORTb 3.0: Improved protein subcellular localization prediction with
@@ -83,7 +98,9 @@
 prokaryotes, Bioinformatics 26(13):1608-1615
 http://dx.doi.org/10.1093/bioinformatics/btq249
 
-http://www.psort.org/documentation/index.html
+See also http://www.psort.org/documentation/index.html
 
+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>