diff variant_combine.xml @ 1:c8752e31f496 draft

Uploaded

--- a/variant_combine.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_combine.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,26 +4,25 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   
-   #set $priority_order = []
-   #for $input_variant in $reference_source.input_variants:
-       -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
-       #set $input_variant_name = str( $input_variant.input_variant_name )
-       #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator
-       #silent $priority_order.append( $input_variant_name )
-   #end for
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+
+    #set $priority_order = []
+    #for $input_variant in $reference_source.input_variants:
+        -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
+        #set $input_variant_name = str( $input_variant.input_variant_name )
+        #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator
+        #silent $priority_order.append( $input_variant_name )
+    #end for
+    -p '
+    @JAR_PATH@
     -T "CombineVariants"
     --out "${output_variants}"
     \$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