changeset 36:14d47237bb0a draft

Fix commandline template
author Jim Johnson <jj@umn.edu>
date Fri, 01 Mar 2013 08:07:56 -0600
parents a29c7d7d962d
children dd9f8ea2b718
files base_recalibrator.xml depth_of_coverage.xml haplotype_caller.xml indel_realigner.xml print_reads.xml realigner_target_creator.xml reduce_reads.xml unified_genotyper.xml variant_annotator.xml variant_apply_recalibration.xml variant_combine.xml variant_eval.xml variant_filtration.xml variant_recalibrator.xml variant_select.xml variants_validate.xml
diffstat 16 files changed, 16 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- 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" ]:
--- 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" ]:
--- 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" ]:
--- 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" ]:
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):
--- 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' ):