Mercurial > repos > jjohnson > gatk2
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(-) [+] |
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--- 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' ):