Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 98:56dbe45f4bfb draft

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author greg
date Thu, 23 Mar 2017 15:01:27 -0400
parents 6154253af263
children de42cdf6e10b
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97:7389c8a99491 98:56dbe45f4bfb
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #set input_format = $input_format_cond.input_format 10 #set input_format = $input_format_cond.input_format
11 #set scaffold = $input_format_cond.scaffold 11 #set scaffold = $input_format_cond.scaffold
12 #set method = $input_format_cond.method 12 #set method = $input_format_cond.method
13 #set options_type_cond = $input_format_cond.options_type_cond 13
14 #if str($input_format) == 'ptortho':
15 #set options_type_cond = $input_format_cond.options_type_cond
16 #else:
17 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
18 #set orthogroup_fna= $orthogroup_fna_cond.orthogroup_fna
19 #set options_type_cond = $orthogroup_fna_cond.options_type_cond
20 #endif
14 #set options_type= $options_type_cond.options_type 21 #set options_type= $options_type_cond.options_type
15 22
16 #if str($options_type) == 'advanced': 23 #if str($options_type) == 'advanced':
17 #set multiple_sequence_alignments_cond = $options_type_cond.multiple_sequence_alignments_cond 24 #if str($input_format) == 'ptortho':
18 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments 25 @REMOVE_GAPPY_SEQUENCES_COND@
19 #if str($multiple_sequence_alignments) == 'yes': 26 @SET_PHYLOGENETIC_TREES@
20 #set multiple_sequence_alignments_option_cond = $options_type_cond.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 27 #if str($phylogenetic_trees) == 'yes':
21 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option 28 @TREE_INFERENCE_COND@
22 #end if 29 #set sequence_type = 'protein'
23 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond 30 #end if
24 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
25 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
26 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
27 #if str(input_format) == 'ptortho':
28 #set sequence_type = 'protein'
29 #else: 31 #else:
30 #set sequence_type = $phylogenetic_trees_cond.sequence_type 32 ## str($input_format) == 'ptorthocs'
31 #set orthogroup_fna = $input_format_cond.orthogroup_fna 33 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
34 #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna
35 #set options_type_cond = orthogroup_fna_cond.options_type_cond
36 #set options_type = $options_type_cond.options_type
37 #if str($orthogroup_fna) == 'yes':
38 #if str(options_type) == 'advanced':
39 @REMOVE_GAPPY_SEQUENCES_COND@
40 #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments
41 @SET_PHYLOGENETIC_TREES@
42 #if str($phylogenetic_trees) == 'yes':
43 @TREE_INFERENCE_COND@
44 #set sequence_type = $phylogenetic_trees_cond.sequence_type
45 #end if
46 #end if
47 #else:
48 #if str(options_type) == 'advanced':
49 @REMOVE_GAPPY_SEQUENCES_COND@
50 @SET_PHYLOGENETIC_TREES@
51 #if str($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
32 #end if 57 #end if
33 #end if 58 #end if
34 59
35 python $__tool_directory__/phylogenomics_analysis.py 60 python $__tool_directory__/phylogenomics_analysis.py
36 --num_threads \${GALAXY_SLOTS:-4} 61 --num_threads \${GALAXY_SLOTS:-4}
58 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit 83 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
59 #end if 84 #end if
60 #end if 85 #end if
61 86
62 #if str($phylogenetic_trees) == 'yes': 87 #if str($phylogenetic_trees) == 'yes':
63 #set tree_inference_cond = $options_type_cond.phylogenetic_trees_cond.tree_inference_cond 88 --tree_inference $tree_inference
64 #set tree_inference_method = $tree_inference_cond.tree_inference 89 #if str($tree_inference) == 'raxml':
65 --tree_inference $tree_inference_method
66 #if str($tree_inference_method) == 'raxml':
67 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
68 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
69 #if str($rooting_order_file) == 'yes': 90 #if str($rooting_order_file) == 'yes':
70 --rooting_order '$rooting_order_file_cond.rooting_order' 91 --rooting_order '$rooting_order_file_cond.rooting_order'
71 # No else block needed here because the default rooting_order 92 # No else block needed here because the default rooting_order
72 # configuration will be used if the --rooting_order flag is missing. 93 # configuration will be used if the --rooting_order flag is missing.
73 #end if 94 #end if
77 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size 98 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size
78 --sequence_type $sequence_type 99 --sequence_type $sequence_type
79 #end if 100 #end if
80 101
81 #if str($remove_gappy_sequences) == 'yes': 102 #if str($remove_gappy_sequences) == 'yes':
82 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
83 #set trim_type = $trim_type_cond.trim_type
84 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
85 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
86 #if str($remove_sequences_with_gaps) == 'yes': 103 #if str($remove_sequences_with_gaps) == 'yes':
87 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of 104 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
88 #end if 105 #end if
89 --trim_type $trim_type_cond.trim_type 106 --trim_type $trim_type_cond.trim_type
90 #if str($trim_type_cond.trim_type) == 'gap_trimming': 107 #if str($trim_type_cond.trim_type) == 'gap_trimming':
124 <expand macro="param_method" /> 141 <expand macro="param_method" />
125 <conditional name="options_type_cond"> 142 <conditional name="options_type_cond">
126 <expand macro="param_options_type" /> 143 <expand macro="param_options_type" />
127 <when value="basic" /> 144 <when value="basic" />
128 <when value="advanced"> 145 <when value="advanced">
146 <expand macro="cond_remove_gappy_sequences" />
129 <expand macro="cond_phylogenetic_trees_ptortho" /> 147 <expand macro="cond_phylogenetic_trees_ptortho" />
130 <expand macro="cond_remove_gappy_sequences" />
131 </when> 148 </when>
132 </conditional> 149 </conditional>
133 </when> 150 </when>
134 <when value="ptorthocs"> 151 <when value="ptorthocs">
135 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" /> 152 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />