diff tools/protein_analysis/promoter2.xml @ 17:e6cc27d182a8 draft

Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS

--- a/tools/protein_analysis/promoter2.xml	Wed Sep 18 06:16:58 2013 -0400
+++ b/tools/protein_analysis/promoter2.xml	Fri Nov 21 08:19:09 2014 -0500
@@ -1,13 +1,10 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.6">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.8">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
     <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
     <command interpreter="python">
-        promoter2.py "\$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 $NSLOTS environment variable.
+        promoter2.py "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file"
         ##If the environment variable isn't set, get "", and the python wrapper
         ##defaults to four threads.
     </command>
@@ -85,4 +82,8 @@
 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>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/15.5.356</citation>
+    </citations>
 </tool>