diff tools/protein_analysis/psortb.xml @ 17:e6cc27d182a8 draft

Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS

--- a/tools/protein_analysis/psortb.xml	Wed Sep 18 06:16:58 2013 -0400
+++ b/tools/protein_analysis/psortb.xml	Fri Nov 21 08:19:09 2014 -0500
@@ -1,14 +1,11 @@
-<tool id="Psortb" name="psortb" version="0.0.3">
+<tool id="Psortb" name="psortb" version="0.0.5">
   <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"
-    ##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 $NSLOTS environment variable.
+    psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
     ##If the environment variable isn't set, get "", and python wrapper
     ##defaults to four threads.
   </command>
@@ -19,9 +16,9 @@
   </stdio>
   <inputs>
     <param format="fasta" name="sequence" type="data"
-	   label="Input sequences for which to predict localisation (protein FASTA format)" />
+           label="Input sequences for which to predict localisation (protein FASTA format)" />
     <param name="type" type="select"
-	   label="Organism type (N.B. all sequences in the above file must be of the same type)" >
+           label="Organism type (N.B. all sequences in the above file must be of the same type)" >
       <option value="-p">Gram positive bacteria</option>
       <option value="-n">Gram negative bacteria</option>
       <option value="-a">Archaea</option>
@@ -34,11 +31,11 @@
       <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
     </param>
     <param name="cutoff" size="10" type="float" optional="true" value=""
-	   label="Sets a cutoff value for reported results (e.g. 7.5)"
-	   help="Leave blank or use zero for no cutoff." />
+           label="Sets a cutoff value for reported results (e.g. 7.5)"
+           help="Leave blank or use zero for no cutoff." />
     <param name="divergent" size="10" type="float" optional="true" value=""
-	   label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
-	   help="Leave blank or use zero for no cutoff." />
+           label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
+           help="Leave blank or use zero for no cutoff." />
   </inputs>
   <outputs>
     <data format="tabular" name="outfile" />
@@ -102,5 +99,9 @@
 
 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
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/btq249</citation>
+    </citations>
   </help>
 </tool>