Mercurial > repos > peterjc > tmhmm_and_signalp

diff tools/protein_analysis/tmhmm2.xml @ 7:9b45a8743100 draft

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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.
author peterjc
date Mon, 30 Jul 2012 10:25:07 -0400
parents a290c6d4e658
children e52220a9ddad
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--- a/tools/protein_analysis/tmhmm2.xml	Tue Jun 07 18:07:09 2011 -0400
+++ b/tools/protein_analysis/tmhmm2.xml	Mon Jul 30 10:25:07 2012 -0400
@@ -1,8 +1,13 @@
-<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.7">
+<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.8">
     <description>Find transmembrane domains 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">
-      tmhmm2.py 8 $fasta_file $tabular_file
-      ##I want the number of threads to be a Galaxy config option...
+      tmhmm2.py "\$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"/>