--- a/reduce_reads.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/reduce_reads.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,15 +4,15 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-   #end if
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+    #end if
+    -p '
+    @JAR_PATH@
     -T "ReduceReads"
     -o "${output_bam}"
 
@@ -22,7 +22,7 @@
     --num_cpu_threads_per_data_thread 1
 
     @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