--- a/base_recalibrator.xml	Mon Dec 02 10:37:45 2013 -0500
+++ b/base_recalibrator.xml	Sat Jan 18 07:00:26 2014 -0500
@@ -17,9 +17,8 @@
     \$GATK2_SITE_OPTIONS
 
     ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
-    --num_cpu_threads_per_data_thread 8
+    --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-8}
 
-    @THREADS@
     ## we set non standards at every run and the user can choose which ones are preferred
     ## in our select box both standard options (ContextCovariate, CycleCovariate) are selected by default
     --no_standard_covs
@@ -111,12 +110,7 @@
         </param>
       </when>
     </conditional>
-    <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" >
-      <help>The input covariates table file which enables on-the-fly base quality score recalibration.
-            Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool.
-            Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
-      </help>
-    </param>
+    <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="The input covariates table file which enables on-the-fly base quality score recalibration. Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. Please be aware that one should only run recalibration with the covariates file created on the same input bam(s) (-BQSR,--BQSR &amp;lt;recal_file&amp;gt;)" />
 
     <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
       <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->