--- a/reduce_reads.xml	Mon Dec 02 10:37:45 2013 -0500
+++ b/reduce_reads.xml	Sat Jan 18 07:00:26 2014 -0500
@@ -21,8 +21,6 @@
     ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
     --num_cpu_threads_per_data_thread 1
 
-    @THREADS@
-
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
@@ -68,12 +66,7 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" 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="csv" 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;)" />
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
@@ -228,8 +221,6 @@
  -noclip_ad / --dont_hardclip_adaptor_sequences ( boolean with default value false )
  Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases.
 
-------
-
 @CITATION_SECTION@
   </help>
 </tool>