--- a/variant_recalibrator.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_recalibrator.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,20 +4,19 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   #for $var_count, $variant in enumerate( $reference_source.variants ):
-      -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
-   #end for
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #for $var_count, $variant in enumerate( $reference_source.variants ):
+        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+    #end for
+    -p '
+    @JAR_PATH@
     -T "VariantRecalibrator"
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if