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comparison phylogenomics_analysis.xml @ 60:29530d7a2a3d draft

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Uploaded
author greg
date Thu, 16 Feb 2017 09:26:48 -0500
parents 963f84101cdc
children bf5cfbf2cfbc
comparison
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59:963f84101cdc 60:29530d7a2a3d
70 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 70 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
71 #else: 71 #else:
72 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 72 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
73 --orthogroup_fna 73 --orthogroup_fna
74 #end if 74 #end if
75 --config_dir '$scaffold.fields.path'
75 --scaffold '$scaffold.fields.path' 76 --scaffold '$scaffold.fields.path'
76 --method $method 77 --method $method
77 78
78 #if str($options_type.options_type_selector) == 'advanced': 79 #if str($options_type.options_type_selector) == 'advanced':
79 #if str($multiple_sequence_alignments) == 'yes': 80 #if str($multiple_sequence_alignments) == 'yes':
95 #if str($tree_inference_method) == 'raxml': 96 #if str($tree_inference_method) == 'raxml':
96 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 97 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
97 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 98 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
98 #if str($rooting_order_file) == 'yes': 99 #if str($rooting_order_file) == 'yes':
99 --rooting_order '$rooting_order_file_cond.rooting_order' 100 --rooting_order '$rooting_order_file_cond.rooting_order'
100 #else: 101 # Noe else block needed here because the default rooting_order
101 #set default_rooting_order = $os.path.join($__tool_directory__, 'rooting_order.config') 102 # configuration will be used if the --rooting_order flag is missing.
102 --rooting_order '$default_rooting_order'
103 #end if 103 #end if
104 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates 104 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
105 #end if 105 #end if
106 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size 106 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
107 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size 107 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size