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comparison macros.xml @ 99:de42cdf6e10b draft

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author greg
date Mon, 27 Mar 2017 09:57:54 -0400
parents 56dbe45f4bfb
children 283f6666daf7
comparison
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98:56dbe45f4bfb 99:de42cdf6e10b
11 <exit_code range=":-1"/> 11 <exit_code range=":-1"/>
12 <regex match="Error:"/> 12 <regex match="Error:"/>
13 <regex match="Exception:"/> 13 <regex match="Exception:"/>
14 </stdio> 14 </stdio>
15 </xml> 15 </xml>
16 <token name="@REMOVE_GAPPY_SEQUENCES_COND@"> 16 <token name="@REMOVE_GAPPY_SEQUENCES_COND_PREP@">
17 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond 17 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
18 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 18 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
19 #if str($remove_gappy_sequences) == 'no': 19 #if str($remove_gappy_sequences) == 'no':
20 #set multiple_sequence_alignments_cond = $remove_gappy_sequences_cond.multiple_sequence_alignments_cond 20 #set multiple_sequence_alignments_cond = $remove_gappy_sequences_cond.multiple_sequence_alignments_cond
21 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments 21 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
51 #if str($multiple_sequence_alignments) == 'yes': 51 #if str($multiple_sequence_alignments) == 'yes':
52 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 52 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
53 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option 53 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
54 #if str($multiple_sequence_alignments_option) == 'pasta_alignments': 54 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
55 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit 55 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
56 #else if str($multiple_sequence_alignments_option) == 'iterative_realignments': 56 #else if str($multiple_sequence_alignments_option) == 'iterative_realignment':
57 #set iterative_realignments = $multiple_sequence_alignments_option_cond.iterative_realignments 57 #set iterative_realignment = $multiple_sequence_alignments_option_cond.iterative_realignment
58 #end if 58 #end if
59 #end if 59 #end if
60 #end if 60 #end if
61 #end if 61 #end if
62 </token> 62 </token>
63 <token name="@SET_PHYLOGENETIC_TREES@"> 63 <token name="@REMOVE_GAPPY_SEQUENCES_COND_CMD@">
64 #if str($remove_gappy_sequences) == 'no':
65 #if str($multiple_sequence_alignments) == 'yes':
66 --alignments_method $multiple_sequence_alignments_option
67 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
68 --pasta_script_path '$__tool_directory__/run_pasta.py'
69 --pasta_iter_limit $pasta_iter_limit
70 #end if
71 #end if
72 #else:
73 ## str($remove_gappy_sequences) == 'yes':
74 --trim_type $trim_type
75 #if str($trim_type) == 'gap_trimming':
76 --gap_trimming $gap_trimming
77 #end if
78 #if str($remove_sequences_with_gaps) == 'no':
79 #if str($multiple_sequence_alignments) == 'yes':
80 --alignments_method $multiple_sequence_alignments_option
81 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
82 --pasta_script_path '$__tool_directory__/run_pasta.py'
83 --pasta_iter_limit $pasta_iter_limit
84 #end if
85 #end if
86 #else:
87 ## str($remove_sequences_with_gaps) == 'yes':
88 --remove_sequences $remove_sequences_with_gaps_of
89 #if str($multiple_sequence_alignments) == 'yes':
90 --alignments_method $multiple_sequence_alignments_option
91 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
92 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
93 --pasta_script_path '$__tool_directory__/run_pasta.py'
94 --pasta_iter_limit $pasta_iter_limit
95 #else:
96 --iterative_realignment $iterative_realignment
97 #end if
98 #end if
99 #end if
100 #end if
101 </token>
102 <token name="@SET_PHYLOGENETIC_TREES_PREP@">
64 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond 103 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond
65 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees 104 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
66 </token> 105 </token>
67 <token name="@TREE_INFERENCE_COND@"> 106 <token name="@TREE_INFERENCE_COND_PREP@">
68 #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond 107 #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
69 #set tree_inference = $tree_inference_cond.tree_inference 108 #set tree_inference = $tree_inference_cond.tree_inference
70 #if str($tree_inference) == 'raxml': 109 #if str($tree_inference) == 'raxml':
71 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 110 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
72 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 111 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
73 #if str($rooting_order_file) == 'yes': 112 #if str($rooting_order_file) == 'yes':
74 #set rooting_order = $rooting_order_file_cond.rooting_order 113 #set rooting_order = $rooting_order_file_cond.rooting_order
75 #end if 114 #end if
76 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates 115 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
77 #end if 116 #end if
117 #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size
78 #set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size 118 #set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size
79 #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size 119 </token>
120 <token name="@TREE_INFERENCE_COND_CMD@">
121 --tree_inference $tree_inference
122 #if str($tree_inference) == 'raxml':
123 #if str($rooting_order_file) == 'yes':
124 --rooting_order '$rooting_order'
125 ## No else block needed here because the default rooting_order
126 ## configuration will be used if the --rooting_order flag is missing.
127 #end if
128 --bootstrap_replicates $bootstrap_replicates
129 #end if
130 --min_orthogroup_size $min_orthogroup_size
131 --max_orthogroup_size $max_orthogroup_size
80 </token> 132 </token>
81 <xml name="param_scaffold"> 133 <xml name="param_scaffold">
82 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 134 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
83 <options from_data_table="plant_tribes_scaffolds" /> 135 <options from_data_table="plant_tribes_scaffolds" />
84 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." /> 136 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
140 <xml name="param_multiple_sequence_alignments_option"> 192 <xml name="param_multiple_sequence_alignments_option">
141 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments"> 193 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
142 <expand macro="options_multiple_sequence_alignments_option" /> 194 <expand macro="options_multiple_sequence_alignments_option" />
143 </param> 195 </param>
144 </xml> 196 </xml>
145 <xml name="param_multiple_sequence_alignments_option_with_iterative_realignments"> 197 <xml name="param_multiple_sequence_alignments_option_with_iterative_realignment">
146 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments"> 198 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
147 <expand macro="options_multiple_sequence_alignments_option" /> 199 <expand macro="options_multiple_sequence_alignments_option" />
148 <option value="iterative_realignments">Iterative orthogroups realignment, trimming and fitering</option> 200 <option value="iterative_realignment">Iterative orthogroups realignment, trimming and fitering</option>
149 </param> 201 </param>
150 </xml> 202 </xml>
151 <xml name="whens_multiple_sequence_alignments_option_cond"> 203 <xml name="whens_multiple_sequence_alignments_option_cond">
152 <when value="create_alignments" /> 204 <when value="create_alignments" />
153 <when value="add_alignments" /> 205 <when value="add_alignments" />
165 <expand macro="whens_multiple_sequence_alignments_option_cond" /> 217 <expand macro="whens_multiple_sequence_alignments_option_cond" />
166 </conditional> 218 </conditional>
167 </when> 219 </when>
168 </conditional> 220 </conditional>
169 </xml> 221 </xml>
170 <xml name="cond_multiple_sequence_alignments_with_iterative_realignments"> 222 <xml name="cond_multiple_sequence_alignments_with_iterative_realignment">
171 <conditional name="multiple_sequence_alignments_cond"> 223 <conditional name="multiple_sequence_alignments_cond">
172 <expand macro="param_multiple_sequence_alignments" /> 224 <expand macro="param_multiple_sequence_alignments" />
173 <when value="no" /> 225 <when value="no" />
174 <when value="yes"> 226 <when value="yes">
175 <conditional name="multiple_sequence_alignments_option_cond"> 227 <conditional name="multiple_sequence_alignments_option_cond">
176 <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignments" /> 228 <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignment" />
177 <expand macro="whens_multiple_sequence_alignments_option_cond" /> 229 <expand macro="whens_multiple_sequence_alignments_option_cond" />
178 <when value="iterative_realignments"> 230 <when value="iterative_realignment">
179 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/> 231 <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
180 </when> 232 </when>
181 </conditional> 233 </conditional>
182 </when> 234 </when>
183 </conditional> 235 </conditional>
184 </xml> 236 </xml>
280 <when value="no"> 332 <when value="no">
281 <expand macro="cond_multiple_sequence_alignments" /> 333 <expand macro="cond_multiple_sequence_alignments" />
282 </when> 334 </when>
283 <when value="yes"> 335 <when value="yes">
284 <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" /> 336 <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
285 <expand macro="cond_multiple_sequence_alignments_with_iterative_realignments" /> 337 <expand macro="cond_multiple_sequence_alignments_with_iterative_realignment" />
286 </when> 338 </when>
287 </conditional> 339 </conditional>
288 </when> 340 </when>
289 </conditional> 341 </conditional>
290 </xml> 342 </xml>