Mercurial > repos > jjohnson > gatk2
comparison variant_annotator.xml @ 36:14d47237bb0a draft
Fix commandline template
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 01 Mar 2013 08:07:56 -0600 |
| parents | a29c7d7d962d |
| children |
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| 35:a29c7d7d962d | 36:14d47237bb0a |
|---|---|
| 85 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] | 85 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] |
| 86 #for $read_filter in $gatk_param_type.read_filter: | 86 #for $read_filter in $gatk_param_type.read_filter: |
| 87 -p ' | 87 -p ' |
| 88 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: | 88 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: |
| 89 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" | 89 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" |
| 90 #end_if | 90 #end if |
| 91 #for $name, $param in $read_filter.read_filter_type.iteritems(): | 91 #for $name, $param in $read_filter.read_filter_type.iteritems(): |
| 92 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: | 92 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: |
| 93 #if hasattr( $param.input, 'truevalue' ): | 93 #if hasattr( $param.input, 'truevalue' ): |
| 94 ${param} | 94 ${param} |
| 95 #else: | 95 #else: |