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comparison print_reads.xml @ 33:76f8ca47b810 draft

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Omit --read_filter param included by default
author Jim Johnson <jj@umn.edu>
date Thu, 28 Feb 2013 15:32:04 -0600
parents 6ef8eb568700
children b99c25b0ad4d
comparison
equal deleted inserted replaced
32:fd9d089a9ff4 33:76f8ca47b810
35 #end for 35 #end for
36 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: 36 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
37 -p '--pedigreeString "${pedigree_string.pedigree_string}"' 37 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
38 #end for 38 #end for
39 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' 39 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
40 #set default_read_filters = ['MalformedReadFilter']
40 #for $read_filter in $gatk_param_type.read_filter: 41 #for $read_filter in $gatk_param_type.read_filter:
41 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 42 -p '
42 ###raise Exception( str( dir( $read_filter ) ) ) 43 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
44 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
45 #end_if
43 #for $name, $param in $read_filter.read_filter_type.iteritems(): 46 #for $name, $param in $read_filter.read_filter_type.iteritems():
44 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 47 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
45 #if hasattr( $param.input, 'truevalue' ): 48 #if hasattr( $param.input, 'truevalue' ):
46 ${param} 49 ${param}
47 #else: 50 #else: