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comparison indel_realigner.xml @ 36:14d47237bb0a draft

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Fix commandline template
author Jim Johnson <jj@umn.edu>
date Fri, 01 Mar 2013 08:07:56 -0600
parents a29c7d7d962d
children
comparison
equal deleted inserted replaced
35:a29c7d7d962d 36:14d47237bb0a
50 #set default_read_filters = ['MalformedRead'] 50 #set default_read_filters = ['MalformedRead']
51 #for $read_filter in $gatk_param_type.read_filter: 51 #for $read_filter in $gatk_param_type.read_filter:
52 -p ' 52 -p '
53 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: 53 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
54 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 54 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
55 #end_if 55 #end if
56 ###raise Exception( str( dir( $read_filter ) ) ) 56 ###raise Exception( str( dir( $read_filter ) ) )
57 #for $name, $param in $read_filter.read_filter_type.iteritems(): 57 #for $name, $param in $read_filter.read_filter_type.iteritems():
58 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 58 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
59 #if hasattr( $param.input, 'truevalue' ): 59 #if hasattr( $param.input, 'truevalue' ):
60 ${param} 60 ${param}