diff tools/protein_analysis/signalp3.xml @ 7:9b45a8743100 draft

Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.

--- a/tools/protein_analysis/signalp3.xml	Tue Jun 07 18:07:09 2011 -0400
+++ b/tools/protein_analysis/signalp3.xml	Mon Jul 30 10:25:07 2012 -0400
@@ -1,8 +1,13 @@
-<tool id="signalp3" name="SignalP 3.0" version="0.0.8">
+<tool id="signalp3" name="SignalP 3.0" version="0.0.9">
     <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 -->
+    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
     <command interpreter="python">
-      signalp3.py $organism $truncate 8 $fasta_file $tabular_file
-      ##I want the number of threads to be a Galaxy config option...
+      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.
     </command>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>