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comparison variant_combine.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
42 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] 42 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead']
43 #for $read_filter in $gatk_param_type.read_filter: 43 #for $read_filter in $gatk_param_type.read_filter:
44 -p ' 44 -p '
45 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: 45 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
46 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 46 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
47 #end_if 47 #end if
48 #for $name, $param in $read_filter.read_filter_type.iteritems(): 48 #for $name, $param in $read_filter.read_filter_type.iteritems():
49 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 49 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
50 #if hasattr( $param.input, 'truevalue' ): 50 #if hasattr( $param.input, 'truevalue' ):
51 ${param} 51 ${param}
52 #else: 52 #else: