Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 99:de42cdf6e10b draft

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Uploaded
author greg
date Mon, 27 Mar 2017 09:57:54 -0400
parents 56dbe45f4bfb
children 283f6666daf7
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98:56dbe45f4bfb 99:de42cdf6e10b
20 #endif 20 #endif
21 #set options_type= $options_type_cond.options_type 21 #set options_type= $options_type_cond.options_type
22 22
23 #if str($options_type) == 'advanced': 23 #if str($options_type) == 'advanced':
24 #if str($input_format) == 'ptortho': 24 #if str($input_format) == 'ptortho':
25 @REMOVE_GAPPY_SEQUENCES_COND@ 25 @REMOVE_GAPPY_SEQUENCES_COND_PREP@
26 @SET_PHYLOGENETIC_TREES@ 26 @SET_PHYLOGENETIC_TREES_PREP@
27 #if str($phylogenetic_trees) == 'yes': 27 #if str($phylogenetic_trees) == 'yes':
28 @TREE_INFERENCE_COND@ 28 @TREE_INFERENCE_COND_PREP@
29 #set sequence_type = 'protein'
30 #end if 29 #end if
31 #else: 30 #else:
32 ## str($input_format) == 'ptorthocs' 31 ## str($input_format) == 'ptorthocs'
33 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond 32 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
34 #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna 33 #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna
35 #set options_type_cond = orthogroup_fna_cond.options_type_cond 34 #set options_type_cond = orthogroup_fna_cond.options_type_cond
36 #set options_type = $options_type_cond.options_type 35 #set options_type = $options_type_cond.options_type
37 #if str($orthogroup_fna) == 'yes': 36 #if str($orthogroup_fna) == 'yes':
38 #if str(options_type) == 'advanced': 37 #if str(options_type) == 'advanced':
39 @REMOVE_GAPPY_SEQUENCES_COND@ 38 @REMOVE_GAPPY_SEQUENCES_COND_PREP@
40 #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments 39 #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments
41 @SET_PHYLOGENETIC_TREES@ 40 @SET_PHYLOGENETIC_TREES_PREP@
42 #if str($phylogenetic_trees) == 'yes': 41 #if str($phylogenetic_trees) == 'yes':
43 @TREE_INFERENCE_COND@ 42 @TREE_INFERENCE_COND_PREP@
43 #end if
44 #end if
45 #else:
46 #if str(options_type) == 'advanced':
47 @REMOVE_GAPPY_SEQUENCES_COND_PREP@
48 @SET_PHYLOGENETIC_TREES_PREP@
49 #if str($phylogenetic_trees) == 'yes':
50 @TREE_INFERENCE_COND_PREP@
44 #set sequence_type = $phylogenetic_trees_cond.sequence_type 51 #set sequence_type = $phylogenetic_trees_cond.sequence_type
45 #end if 52 #end if
46 #end if 53 #end if
47 #else:
48 #if str(options_type) == 'advanced':
49 @REMOVE_GAPPY_SEQUENCES_COND@
50 @SET_PHYLOGENETIC_TREES@
51 #if str($phylogenetic_trees) == 'yes':
52 @TREE_INFERENCE_COND@
53 #set sequence_type = $phylogenetic_trees_cond.sequence_type
54 #end if
55 #end if
56 #end if 54 #end if
57 #end if 55 #end if
58 #end if 56 #end if
59 57
60 python $__tool_directory__/phylogenomics_analysis.py 58 python $__tool_directory__/phylogenomics_analysis.py
59 --config_dir '$scaffold.fields.path'
60 --scaffold '$scaffold.fields.path'
61 --method $method
61 --num_threads \${GALAXY_SLOTS:-4} 62 --num_threads \${GALAXY_SLOTS:-4}
63
62 #if str($input_format) == 'ptortho': 64 #if str($input_format) == 'ptortho':
63 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 65 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
66 #if str($options_type) == 'advanced':
67 @REMOVE_GAPPY_SEQUENCES_COND_CMD@
68 #if str($phylogenetic_trees) == 'yes':
69 @TREE_INFERENCE_COND_CMD@
70 --sequence_type 'protein'
71 #end if
72 #end if
64 #else: 73 #else:
74 ## str($input_format) == 'ptorthocs'
65 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 75 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
66 #if str($orthogroup_fna) == 'yes': 76 #if str($orthogroup_fna) == 'yes':
67 --orthogroup_fna 'true' 77 --orthogroup_fna 'true'
68 #end if 78 #if str(options_type) == 'advanced':
69 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments 79 @REMOVE_GAPPY_SEQUENCES_COND_CMD@
70 #if str($multiple_codon_alignments) == 'yes': 80 #if str($multiple_codon_alignments) == 'yes':
71 --codon_alignments 'true' 81 --codon_alignments 'true'
72 #end if 82 #end if
73 #end if 83 #if str($phylogenetic_trees) == 'yes':
74 --config_dir '$scaffold.fields.path' 84 @TREE_INFERENCE_COND_CMD@
75 --scaffold '$scaffold.fields.path' 85 --sequence_type = $phylogenetic_trees_cond.sequence_type
76 --method $method 86 #end if
77 87 #end if
78 #if str($options_type) == 'advanced': 88 #else:
79 #if str($multiple_sequence_alignments) == 'yes': 89 #if str(options_type) == 'advanced':
80 --alignments_method $multiple_sequence_alignments_option 90 @REMOVE_GAPPY_SEQUENCES_COND_CMD@
81 #if str($multiple_sequence_alignments_option) == 'pasta_alignments': 91 #if str($phylogenetic_trees) == 'yes':
82 --pasta_script_path '$__tool_directory__/run_pasta.py' 92 @TREE_INFERENCE_COND_CMD@
83 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit 93 --sequence_type = $phylogenetic_trees_cond.sequence_type
84 #end if 94 #end if
85 #end if
86
87 #if str($phylogenetic_trees) == 'yes':
88 --tree_inference $tree_inference
89 #if str($tree_inference) == 'raxml':
90 #if str($rooting_order_file) == 'yes':
91 --rooting_order '$rooting_order_file_cond.rooting_order'
92 # No else block needed here because the default rooting_order
93 # configuration will be used if the --rooting_order flag is missing.
94 #end if
95 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
96 #end if
97 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size
98 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size
99 --sequence_type $sequence_type
100 #end if
101
102 #if str($remove_gappy_sequences) == 'yes':
103 #if str($remove_sequences_with_gaps) == 'yes':
104 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
105 #end if
106 --trim_type $trim_type_cond.trim_type
107 #if str($trim_type_cond.trim_type) == 'gap_trimming':
108 --gap_trimming $trim_type_cond.gap_trimming
109 #end if 95 #end if
110 #end if 96 #end if
111 #end if 97 #end if
112 98
113 #if str($input_format) == 'ptortho': 99 #if str($input_format) == 'ptortho':