# HG changeset patch
# User peterjc
# Date 1382004251 14400
# Node ID c2f64216ff1d6a4cd9dace79720ed8e3ec350530
# Parent  0d39248a7a9fa827470a0d32d9e010c073f3155e
Uploaded v0.0.7, support for $GALAXY_SLOTS

diff -r 0d39248a7a9f -r c2f64216ff1d tools/clinod/README.rst
--- a/tools/clinod/README.rst	Tue Sep 17 11:43:15 2013 -0400
+++ b/tools/clinod/README.rst	Thu Oct 17 06:04:11 2013 -0400
@@ -67,6 +67,7 @@
         - Use reStructuredText for this README file.
         - Updated citation information (Cock et al. 2013).
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.7  - Use the new $GALAXY_SLOTS environment variable for thread count.
 ======= ======================================================================
 
 
diff -r 0d39248a7a9f -r c2f64216ff1d tools/clinod/clinod.xml
--- a/tools/clinod/clinod.xml	Tue Sep 17 11:43:15 2013 -0400
+++ b/tools/clinod/clinod.xml	Thu Oct 17 06:04:11 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="binary">java</requirement>
@@ -7,8 +7,7 @@
     <command>
 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
 ##containing both clinod-1.3.jar and the batchman binary:
-java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence
-##I want the number of threads to be a Galaxy config option...
+java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
 ##TODO - Make the -clean_sequence argument a parameter?
     </command>
     <stdio>