Mercurial > repos > greg > plant_tribes_gene_family_classifier

comparison gene_family_classifier.xml @ 1:95cb5d32a3b4 draft

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Uploaded
author greg
date Tue, 01 Aug 2017 14:25:47 -0400
parents f8603464bea7
children 8ec75782a05b
comparison
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0:f8603464bea7 1:95cb5d32a3b4
41 #set single_copy_orthogroup = False 41 #set single_copy_orthogroup = False
42 #set create_ortho_sequences = False 42 #set create_ortho_sequences = False
43 #set create_corresponding_coding_sequences = False 43 #set create_corresponding_coding_sequences = False
44 #end if 44 #end if
45 45
46 python $__tool_directory__/gene_family_classifier.py 46 python '$__tool_directory__/gene_family_classifier.py'
47 --input '$input' 47 --input '$input'
48 --scaffold '$scaffold.fields.path' 48 --scaffold '$scaffold.fields.path'
49 --method $method 49 --method $method
50 --classifier $save_hmmscan_log_cond.classifier 50 --classifier $save_hmmscan_log_cond.classifier
51 --config_dir '$scaffold.fields.path' 51 --config_dir '$scaffold.fields.path'
58 #if $single_copy_orthogroup: 58 #if $single_copy_orthogroup:
59 #if str($single_copy) == 'custom': 59 #if str($single_copy) == 'custom':
60 #set single_copy_custom_cond = $single_copy_cond.single_copy_custom_cond 60 #set single_copy_custom_cond = $single_copy_cond.single_copy_custom_cond
61 #set single_copy_custom = $single_copy_custom_cond.single_copy_custom 61 #set single_copy_custom = $single_copy_custom_cond.single_copy_custom
62 #if str($single_copy_custom) == 'no': 62 #if str($single_copy_custom) == 'no':
63 --single_copy_custom 'default' 63 --single_copy_custom default
64 #else: 64 #else:
65 --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config' 65 --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config'
66 #end if 66 #end if
67 #else: 67 #else:
68 #if str($single_copy_cond.single_copy_taxa): 68 #if str($single_copy_cond.single_copy_taxa):
72 --taxa_present $single_copy_cond.taxa_present 72 --taxa_present $single_copy_cond.taxa_present
73 #end if 73 #end if
74 #end if 74 #end if
75 #end if 75 #end if
76 #if $create_ortho_sequences: 76 #if $create_ortho_sequences:
77 --orthogroup_fasta "true" 77 --orthogroup_fasta true
78 #if $create_corresponding_coding_sequences: 78 #if $create_corresponding_coding_sequences:
79 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences' 79 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences'
80 #end if 80 #end if
81 #end if 81 #end if
82 #end if 82 #end if
83 83
84 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': 84 #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
85 --save_hmmscan_log 'true' 85 --save_hmmscan_log true
86 --hmmscan_log '$hmmscan_log' 86 --hmmscan_log '$hmmscan_log'
87 #end if 87 #end if
88 #if $create_ortho_sequences: 88 #if $create_ortho_sequences:
89 #if $create_corresponding_coding_sequences: 89 #if $create_corresponding_coding_sequences:
90 --output_ptorthocs '$output_ptorthocs' 90 --output_ptorthocs '$output_ptorthocs'