# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1362146876 21600
# Node ID 14d47237bb0aa4dd71de522b3685082d5d64bed9
# Parent  a29c7d7d962d7dd91d95f6f311cdb15efe582049
Fix commandline template

diff -r a29c7d7d962d -r 14d47237bb0a base_recalibrator.xml
--- a/base_recalibrator.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/base_recalibrator.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -66,7 +66,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             ###raise Exception( str( dir( $read_filter ) ) )
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
diff -r a29c7d7d962d -r 14d47237bb0a depth_of_coverage.xml
--- a/depth_of_coverage.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/depth_of_coverage.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -53,7 +53,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             ###raise Exception( str( dir( $read_filter ) ) )
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
diff -r a29c7d7d962d -r 14d47237bb0a haplotype_caller.xml
--- a/haplotype_caller.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/haplotype_caller.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -41,7 +41,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             ###raise Exception( str( dir( $read_filter ) ) )
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
diff -r a29c7d7d962d -r 14d47237bb0a indel_realigner.xml
--- a/indel_realigner.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/indel_realigner.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -52,7 +52,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             ###raise Exception( str( dir( $read_filter ) ) )
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
diff -r a29c7d7d962d -r 14d47237bb0a print_reads.xml
--- a/print_reads.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/print_reads.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -42,7 +42,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a realigner_target_creator.xml
--- a/realigner_target_creator.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/realigner_target_creator.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -49,7 +49,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a reduce_reads.xml
--- a/reduce_reads.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/reduce_reads.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -42,7 +42,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a unified_genotyper.xml
--- a/unified_genotyper.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/unified_genotyper.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -56,7 +56,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variant_annotator.xml
--- a/variant_annotator.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variant_annotator.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -87,7 +87,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variant_apply_recalibration.xml
--- a/variant_apply_recalibration.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variant_apply_recalibration.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -38,7 +38,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variant_combine.xml
--- a/variant_combine.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variant_combine.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -44,7 +44,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variant_eval.xml
--- a/variant_eval.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variant_eval.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -52,7 +52,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variant_filtration.xml
--- a/variant_filtration.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variant_filtration.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -48,7 +48,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variant_recalibrator.xml
--- a/variant_recalibrator.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variant_recalibrator.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -56,7 +56,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variant_select.xml
--- a/variant_select.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variant_select.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -108,7 +108,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r a29c7d7d962d -r 14d47237bb0a variants_validate.xml
--- a/variants_validate.xml	Fri Mar 01 07:52:02 2013 -0600
+++ b/variants_validate.xml	Fri Mar 01 08:07:56 2013 -0600
@@ -41,7 +41,7 @@
             -p '
             #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            #end_if
+            #end if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):