diff variant_validate.xml @ 1:c8752e31f496 draft

Uploaded

--- a/variant_validate.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_validate.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,8 +4,8 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
+  <command interpreter="python">
+    gatk2_wrapper.py
    --stdout "${output_log}"
    -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
    -p '
@@ -15,7 +15,7 @@
     \$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
@@ -27,7 +27,7 @@
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
     #end if
    
-    #include source=$standard_gatk_options#    
+    #include source=$standard_gatk_options#
   </command>
   <inputs>