Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 13:521d09ac701a draft

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author greg
date Tue, 31 Jan 2017 13:55:22 -0500
parents 622603f41432
children b468a86f87d9
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12:622603f41432 13:521d09ac701a
20 #if str($prediction_method_cond.prediction_method) == 'estscan': 20 #if str($prediction_method_cond.prediction_method) == 'estscan':
21 --score_matrices '$score_matrices' 21 --score_matrices '$score_matrices'
22 #end if 22 #end if
23 #if str($options_type.options_type_selector) == 'advanced': 23 #if str($options_type.options_type_selector) == 'advanced':
24 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 24 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
25 #set scaffold_path = $options_type.target_gene_family_assembly_cond.scaffold['path'] 25 #set scaffold_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
26 #set scaffold_dir = $os.path.split($scaffold_path)[0] 26 #set scaffold_dir = $os.path.split($scaffold_path)[0]
27 #set scaffold = $os.path.split($scaffold_path)[1] 27 #set scaffold = $os.path.split($scaffold_path)[1]
28 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups' 28 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
29 --scaffold_dir $scaffold_dir 29 --scaffold_dir $scaffold_dir
30 --scaffold $scaffold 30 --scaffold $scaffold