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comparison raxml.xml @ 1:ba29b5e2a4be draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
author iuc
date Tue, 27 Jun 2017 16:27:39 -0400
parents 6805e85573b8
children a4b71be30c3c
comparison
equal deleted inserted replaced
0:6805e85573b8 1:ba29b5e2a4be
1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.2"> 1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4">
2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description> 2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
3 <requirements> 3 <requirements>
4 <requirement type='package' version="8.2.4">raxml</requirement> 4 <requirement type="package" version="8.2.4">raxml</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">raxml.py 6 <command detect_errors="exit_code"><![CDATA[
7 ## Required parameters 7 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
8 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 8 #set $slots = $getVar('GALAXY_SLOTS', 1)
9 ## (-T) 9 #if $slots == 1:
10 ## Cannot have --threads 1 10 raxmlHPC
11 #set $slots = $getVar('GALAXY_SLOTS', 1) 11 ## Cannot have -T 1
12 #if $slots == 1: 12 #else:
13 --binary "raxmlHPC" 13 raxmlHPC-PTHREADS
14 --threads 1 14 -T $slots
15 #end if
16 -s '$infile'
17 -n galaxy
18 #if $search_model_selector.model_type == 'aminoacid':
19 -m ${search_model_selector.base_model}${search_model_selector.aa_search_matrix}${search_model_selector.aa_model_empirical_base_frequencies}
20 #else:
21 -m $search_model_selector.base_model
22 #end if
23 -p $random_seed
24
25 #if $selExtraOpts.extraOptions == 'full':
26 #if $selExtraOpts.number_of_runs_conditional.number_of_runs_selector == 'by_number_of_runs':
27 -N $selExtraOpts.number_of_runs_conditional.number_of_runs
15 #else: 28 #else:
16 --binary "raxmlHPC-PTHREADS" 29 -N $selExtraOpts.number_of_runs_conditional.number_of_runs_bootstop
17 --threads $slots 30 #end if
18 #end if 31 #if $selExtraOpts.weightfile:
19 ## (-s) 32 -a '$selExtraOpts.weightfile'
20 --source "$infile" 33 #end if
21 ## (-m) 34 #if $selExtraOpts.secondary_structure_model:
22 --model_type $search_model_selector.model_type 35 -A $selExtraOpts.secondary_structure_model
23 --base_model $search_model_selector.base_model 36 #end if
24 #if str( $search_model_selector.model_type ) == 'aminoacid': 37 #if str($selExtraOpts.bootseed):
25 $search_model_selector.aa_model_empirical_base_frequencies 38 -b $selExtraOpts.bootseed
26 #if $search_model_selector.aa_search_matrix: 39 #end if
27 --aa_search_matrix $search_model_selector.aa_search_matrix 40 -B $selExtraOpts.cutoff_threshold
28 #end if 41 -c $selExtraOpts.numofcats
29 #end if 42 $selExtraOpts.search_complete_random_tree
30 43 $selExtraOpts.ml_search_convergence
31 ## Optional parameters 44 #if $selExtraOpts.model_opt_precision:
32 45 -e $selExtraOpts.model_opt_precision
33 #if str( $selExtraOpts.extraOptions ) == 'full': 46 #end if
34 ## (-N/#) 47 #if $selExtraOpts.excludefile:
35 #if $selExtraOpts.number_of_runs: 48 -E '$selExtraOpts.excludefile'
36 --number_of_runs $selExtraOpts.number_of_runs 49 #end if
37 #end if 50 #if $selExtraOpts.search_algorithm:
38 #if $selExtraOpts.number_of_runs_bootstop: 51 -f $selExtraOpts.search_algorithm
39 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop 52 #end if
40 #end if 53 $selExtraOpts.save_memory_cat_model
41 ## (-a) 54 #if $selExtraOpts.groupingfile:
42 #if $selExtraOpts.weightfile: 55 -g '$selExtraOpts.groupingfile'
43 --weightfile "$selExtraOpts.weightfile" 56 #end if
44 #end if 57 #if $selExtraOpts.enable_evol_heuristics:
45 ## (-b) 58 -G $selExtraOpts.enable_evol_heuristics
46 #if str ($selExtraOpts.secondary_structure_model) != "": 59 #end if
47 --secondary_structure_model $selExtraOpts.secondary_structure_model 60 #if str($selExtraOpts.initial_rearrangement_setting):
48 #end if 61 -i $selExtraOpts.initial_rearrangement_setting
49 ## (-b) 62 #end if
50 #if str($selExtraOpts.bootseed): 63 #if $selExtraOpts.posterior_bootstopping_analysis:
51 --bootseed $selExtraOpts.bootseed 64 -I $selExtraOpts.posterior_bootstopping_analysis
52 #end if 65 #end if
53 ## (-c) 66 #if $selExtraOpts.majority_rule_consensus:
54 #if $selExtraOpts.numofcats: 67 -J $selExtraOpts.majority_rule_consensus
55 --numofcats $selExtraOpts.numofcats 68 #end if
56 #end if 69 $selExtraOpts.print_branch_lengths
57 ## (-d) 70 -K $selExtraOpts.multistate_sub_model
58 $selExtraOpts.search_complete_random_tree 71 $selExtraOpts.estimate_individual_branch_lengths
59 ## (-D) 72 #if $selExtraOpts.outgroup_name:
60 $selExtraOpts.ml_search_convergence 73 -o '$selExtraOpts.outgroup_name'
61 ## (-e) 74 #end if
62 #if $selExtraOpts.model_opt_precision: 75 $selExtraOpts.disable_undetermined_seq_check
63 --model_opt_precision $selExtraOpts.model_opt_precision 76 #if $selExtraOpts.external_protein_model:
64 #end if 77 -P '$selExtraOpts.external_protein_model'
65 ## (-E) 78 #end if
66 #if $selExtraOpts.excludefile: 79 #if $selExtraOpts.multiple_model:
67 --excludefile "$selExtraOpts.excludefile" 80 -q '$selExtraOpts.multiple_model'
68 #end if 81 #end if
69 ## (-f) 82 #if $selExtraOpts.constraint_file:
70 #if $selExtraOpts.search_algorithm: 83 -r '$selExtraOpts.constraint_file'
71 --search_algorithm $selExtraOpts.search_algorithm 84 #end if
72 #end if 85 #if $selExtraOpts.bin_model_parameter_file:
73 ## (-F) 86 -R '$selExtraOpts.bin_model_parameter_file'
74 $selExtraOpts.save_memory_cat_model 87 #end if
75 ## (-g) 88 #if $selExtraOpts.secondary_structure_file:
76 #if $selExtraOpts.groupingfile: 89 -S '$selExtraOpts.secondary_structure_file'
77 --groupingfile "$selExtraOpts.groupingfile" 90 #end if
78 #end if 91 #if $selExtraOpts.start_tree_file:
79 ## (-G) 92 -t '$selExtraOpts.start_tree_file'
80 #if $selExtraOpts.enable_evol_heuristics: 93 #end if
81 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics 94 $selExtraOpts.use_median_approximation
82 #end if 95 $selExtraOpts.save_memory_gappy_alignments
83 ## (-i) 96 $selExtraOpts.disable_rate_heterogeneity
84 #if $selExtraOpts.initial_rearrangement_setting: 97 -W $selExtraOpts.sliding_window_size
85 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting 98 #if str($selExtraOpts.rapid_bootstrap_random_seed):
86 #end if 99 -x $selExtraOpts.rapid_bootstrap_random_seed
87 ## (-I) 100 #end if
88 #if $selExtraOpts.posterior_bootstopping_analysis: 101 $selExtraOpts.parsimony_starting_tree_only
89 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis 102 #end if
90 #end if 103 && python '$__tool_directory__/raxml.py'
91 ## (-J) 104 #if $selExtraOpts.extraOptions == 'full':
92 #if $selExtraOpts.majority_rule_consensus: 105 #if str($selExtraOpts.bootseed):
93 --majority_rule_consensus $selExtraOpts.majority_rule_consensus 106 --bootseed $selExtraOpts.bootseed
94 #end if 107 #end if
95 ## (-k) 108 #if str($selExtraOpts.rapid_bootstrap_random_seed):
96 $selExtraOpts.print_branch_lengths 109 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
97 ## (-K) 110 #end if
98 #if str ($selExtraOpts.multistate_sub_model) != "": 111 #if $selExtraOpts.number_of_runs_conditional.number_of_runs_selector == 'by_number_of_runs':
99 --multistate_sub_model $selExtraOpts.multistate_sub_model 112 --number_of_runs $selExtraOpts.number_of_runs_conditional.number_of_runs
100 #end if 113 #end if
101 ## (-m) - see elsewhere 114 #if $selExtraOpts.multiple_model:
102 ## (-M) 115 --multiple_model '$selExtraOpts.multiple_model'
103 $selExtraOpts.estimate_individual_branch_lengths 116 #end if
104 ## (-n) - see elsewhere 117 #end if
105 ## (-o) 118 ]]></command>
106 #if $selExtraOpts.outgroup_name:
107 --outgroup_name "$selExtraOpts.outgroup_name"
108 #end if
109 ## (-O)
110 $selExtraOpts.disable_undetermined_seq_check
111 ## (-P)
112 #if $selExtraOpts.external_protein_model:
113 --external_protein_model "$selExtraOpts.external_protein_model"
114 #end if
115 ## (-q)
116 #if $selExtraOpts.multiple_model:
117 --multiple_model "$selExtraOpts.multiple_model"
118 #end if
119 ## (-r)
120 #if $selExtraOpts.constraint_file:
121 --constraint_file "$selExtraOpts.constraint_file"
122 #end if
123 ## (-R)
124 #if $selExtraOpts.bin_model_parameter_file:
125 --bin_model_parameter_file "$selExtraOpts.bin_model_parameter_file"
126 #end if
127 ## (-S)
128 #if $selExtraOpts.secondary_structure_file:
129 --secondary_structure_file "$selExtraOpts.secondary_structure_file"
130 #end if
131 ## (-t)
132 #if $selExtraOpts.start_tree_file:
133 --starting_tree "$selExtraOpts.start_tree_file"
134 #end if
135 ## (-T) see elsewhere
136 ## (-u)
137 $selExtraOpts.use_median_approximation
138 ## (-U)
139 $selExtraOpts.save_memory_gappy_alignments
140 ## (-V)
141 $selExtraOpts.disable_rate_heterogeneity
142 ## (-W)
143 #if $selExtraOpts.sliding_window_size:
144 --sliding_window_size $selExtraOpts.sliding_window_size
145 #end if
146 ## (-x)
147 #if str($selExtraOpts.rapid_bootstrap_random_seed):
148 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
149 #end if
150 ## (-y)
151 $selExtraOpts.parsimony_starting_tree_only
152 ## (-z)
153 #if $selExtraOpts.file_multiple_trees:
154 --file_multiple_trees "$selExtraOpts.file_multiple_trees"
155 #end if
156
157 ## (-p)
158 #if $selExtraOpts.random_seed:
159 --random_seed $selExtraOpts.random_seed
160 #else
161 --random_seed 1234567890
162 #end if
163
164 #else:
165 --random_seed 1234567890
166 #end if
167 </command>
168 <inputs> 119 <inputs>
169 <param type="data" format="fasta,phylip" name="infile" label="Source file" help="(-s)"/> 120 <param name="infile" argument="-s" type="data" format="fasta,phylip" label="Source file" />
170 <conditional name="search_model_selector"> 121 <conditional name="search_model_selector">
171 <param name="model_type" type="select" label="Model Type" help="(--model_type)"> 122 <param name="model_type" type="select" label="Model type">
172 <option value="nucleotide" selected="true">Nucleotide</option> 123 <option value="nucleotide" selected="true">Nucleotide</option>
173 <option value="aminoacid">Amino Acid</option> 124 <option value="aminoacid">Amino Acid</option>
174 <option value="binary">Binary</option> 125 <option value="binary">Binary</option>
175 <option value="multistate">Multistate</option> 126 <option value="multistate">Multistate</option>
176 </param> 127 </param>
177 <when value="nucleotide"> 128 <when value="nucleotide">
178 <param name="base_model" type="select" label="Substitution Model" help="--base-model"> 129 <param name="base_model" type="select" label="Substitution model">
179 <option value="GTRCAT">GTRCAT</option> 130 <option value="GTRCAT">GTRCAT</option>
180 <option value="GTRCATI">GTRCATI</option> 131 <option value="GTRCATI">GTRCATI</option>
181 <option value="GTRGAMMA" selected="true">GTRGAMMA</option> 132 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
182 <option value="GTRGAMMAI">GTRGAMMAI</option> 133 <option value="GTRGAMMAI">GTRGAMMAI</option>
183 </param> 134 </param>
184 </when> 135 </when>
185 <when value="aminoacid"> 136 <when value="aminoacid">
186 <param name="aa_model_empirical_base_frequencies" 137 <param name="base_model" type="select" label="Substitution model">
187 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" />
188 <param name="base_model" type="select" label="Substitution Model (--base_model)">
189 <option value="PROTCAT" selected="true">PROTCAT</option> 138 <option value="PROTCAT" selected="true">PROTCAT</option>
190 <option value="PROTCATI">PROTCATI</option> 139 <option value="PROTCATI">PROTCATI</option>
191 <option value="PROTGAMMA">PROTGAMMA</option> 140 <option value="PROTGAMMA">PROTGAMMA</option>
192 <option value="PROTGAMMAI">PROTGAMMAI</option> 141 <option value="PROTGAMMAI">PROTGAMMAI</option>
193 </param> 142 </param>
194 <param name="aa_search_matrix" type="select" label="Matrix" help="(--aa_search_matrix)"> 143 <param name="aa_search_matrix" type="select" label="Matrix">
195 <option value="DAYHOFF" selected="true">DAYHOFF</option> 144 <option value="DAYHOFF" selected="true">DAYHOFF</option>
196 <option value="DCMUT">DCMUT</option> 145 <option value="DCMUT">DCMUT</option>
197 <option value="JTT">JTT</option> 146 <option value="JTT">JTT</option>
198 <option value="MTREV">MTREV</option> 147 <option value="MTREV">MTREV</option>
199 <option value="WAG">WAG</option> 148 <option value="WAG">WAG</option>
213 <option value="DUMMY">DUMMY</option> 162 <option value="DUMMY">DUMMY</option>
214 <option value="DUMMY2">DUMMY2</option> 163 <option value="DUMMY2">DUMMY2</option>
215 <option value="GTR_UNLINKED">GTR_UNLINKED</option> 164 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
216 <option value="GTR">GTR</option> 165 <option value="GTR">GTR</option>
217 </param> 166 </param>
167 <param name="aa_model_empirical_base_frequencies" type="boolean" truevalue="F" falsevalue="" checked="no" display="checkboxes" label="Use empirical base frequencies in AA models" />
218 </when> 168 </when>
219 <when value="binary"> 169 <when value="binary">
220 <param name="base_model" type="select" label="Substitution Model" help="(--base_model)"> 170 <param name="base_model" type="select" label="Substitution model">
221 <option value="BINCAT">BINCAT</option> 171 <option value="BINCAT">BINCAT</option>
222 <option value="BINCATI">BINCATI</option> 172 <option value="BINCATI">BINCATI</option>
223 <option value="BINGAMMA">BINGAMMA</option> 173 <option value="BINGAMMA">BINGAMMA</option>
224 <option value="BINGAMMAI">BINGAMMAI</option> 174 <option value="BINGAMMAI">BINGAMMAI</option>
225 </param> 175 </param>
226 </when> 176 </when>
227 <when value="multistate"> 177 <when value="multistate">
228 <param name="base_model" type="select" label="Substitution Model"> 178 <param name="base_model" type="select" label="Substitution model">
229 <option value="MULTICAT">MULTICAT</option> 179 <option value="MULTICAT">MULTICAT</option>
230 <option value="MULTICATI">MULTICATI</option> 180 <option value="MULTICATI">MULTICATI</option>
231 <option value="MULTIGAMMA">MULTIGAMMA</option> 181 <option value="MULTIGAMMA">MULTIGAMMA</option>
232 <option value="MULTIGAMMAI">MULTIGAMMAI</option> 182 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
233 </param> 183 </param>
234 </when> 184 </when>
235 </conditional> 185 </conditional>
186 <param name="random_seed" argument="-p" type="integer" value="1234567890" label="Random seed used for the parsimony inferences" />
236 <conditional name="selExtraOpts"> 187 <conditional name="selExtraOpts">
237 <param name="extraOptions" type="select" label="RAxML options to use" 188 <param name="extraOptions" type="select" label="RAxML options to use"
238 help="The required minimal settings are the input file and the 189 help="The required minimal settings are the input file and the
239 substitution model. To specify extra options select the 'Full option list'"> 190 substitution model. To specify extra options select the 'Full option list'">
240 <option value="required">Required options only</option> 191 <option value="required">Required options only</option>
241 <option value="full">Full option list</option> 192 <option value="full">Full option list</option>
242 </param> 193 </param>
243 <when value="required" /> 194 <when value="required" />
244 <when value="full"> 195 <when value="full">
245 <param name="number_of_runs" type="integer" value="" 196 <conditional name="number_of_runs_conditional">
246 label="Number of runs" help="Specify the number of 197 <param name="number_of_runs_selector" type="select" label="Multiple boostrap specification">
247 alternative runs (-N|#) on distinct starting trees In combination 198 <option value="by_number_of_runs">By number of runs</option>
248 with the '-b' option will invoke a multiple boostrap analysis. 199 <option value="by_bootstopping">By bootstopping criteria</option>
249 You can add the bootstopping criteria by choosing the autoMR, 200 </param>
250 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of 201 <when value="by_number_of_runs">
251 providing a number here. Bootstopping will only work in 202 <param name="number_of_runs" argument="-N" type="integer" value="1" label="Number of alternative runs on distinct starting trees"
252 combination with '-x' or '-b'." 203 help="In combination with the '-b' option, this will invoke a multiple boostrap analysis" />
253 optional="True" /> 204 </when>
254 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True" help="--number_of_runs_bootstop"> 205 <when value="by_bootstopping">
255 <option value="" selected="yes"></option> 206 <param name="number_of_runs_bootstop" argument="-N" type="select" label="Bootstopping criteria" help="Bootstopping will only work in combination with '-x' or '-b'">
256 <option value="autoMR">autoMR</option> 207 <option value="autoMR">autoMR</option>
257 <option value="autoMRE">autoMRE</option> 208 <option value="autoMRE">autoMRE</option>
258 <option value="autoMRE_IGN">autoMRE_IGN</option> 209 <option value="autoMRE_IGN">autoMRE_IGN</option>
259 <option value="autoFC">autoFC</option> 210 <option value="autoFC">autoFC</option>
260 </param> 211 </param>
261 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" help="(-a)" /> 212 </when>
262 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True" 213 </conditional>
263 help="(--secondary_structure_model)"> 214 <param name="weightfile" argument="-a" type="data" format="txt" optional="true" label="Column weight file" />
264 <option value="" selected="yes"></option> 215 <param name="secondary_structure_model" argument="-A" type="select" optional="true" label="Secondary structure substitution model">
265 <option value="S6A">S6A</option> 216 <option value="S6A">S6A</option>
266 <option value="S6B">S6B</option> 217 <option value="S6B">S6B</option>
267 <option value="S6C">S6C</option> 218 <option value="S6C">S6C</option>
268 <option value="S6D">S6D</option> 219 <option value="S6D">S6D</option>
269 <option value="S6E">S6E</option> 220 <option value="S6E">S6E</option>
275 <option value="S7F">S7F</option> 226 <option value="S7F">S7F</option>
276 <option value="S16">S16</option> 227 <option value="S16">S16</option>
277 <option value="S16A">S16A</option> 228 <option value="S16A">S16A</option>
278 <option value="S16B">S16B</option> 229 <option value="S16B">S16B</option>
279 </param> 230 </param>
280 <param name="bootseed" type="integer" value="" label="Random number for non-parametric bootstrapping" optional="True" help="(--bootseed)"/> 231 <param name="bootseed" argument="-b" type="integer" value="" optional="true" label="Random seed for non-parametric bootstrapping"
281 <param name="rapid_bootstrap_random_seed" type="integer" value='' label="Rapid bootstrapping random seed" optional="True" 232 help="Specifying a value turns on bootstrapping" />
282 help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT. (-x)" /> 233 <param name="rapid_bootstrap_random_seed" argument="-x" type="integer" value="" optional="true" label="Random seed for rapid bootstrapping"
283 <param name="cutoff_threshold" type="float" label="MR Cutoff threshold" value="" 234 help="Specifying a value turns on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT" />
284 help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1. (-B)" optional="True"/> 235 <param name="cutoff_threshold" argument="-B" type="float" value="0.03" min="0" max="1" label="MR cutoff threshold"
285 <param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" help="(-c)" /> 236 help="Cutoff threshold for the MR-based bootstopping criteria" />
237 <param name="numofcats" argument="-c" type="integer" value="25" label="Number of Rate Categories for GTRCAT/GTRMIX" />
286 <!-- (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. --> 238 <!-- (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. -->
287 <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="--search_complete_random_tree" falsevalue="" 239 <param name="search_complete_random_tree" argument="-d" type="boolean" truevalue="-d" falsevalue=""
288 display="checkboxes" label="Start ML optimization from a complete random starting tree" help="(--search_complete_random_tree)"/> 240 label="Start ML optimization from a complete random starting tree" />
289 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" 241 <param name="ml_search_convergence" argument="-D" type="boolean" truevalue="-D" falsevalue=""
290 label="ML search convergence criterion" help="(--ml_search_convergence)" /> 242 label="ML search convergence criterion" help="This will break off ML searches if the relative Robinson-Foulds distance between the trees obtained from two consecutive lazy SPR cycles is smaller or equal to 1%. Usage recommended for very large datasets in terms of taxa. On trees with more than 500 taxa this will yield execution time improvements of approximately 50% while yielding only slightly worse trees" />
291 <param name="model_opt_precision" type="float" label="Model optimization precision" value="" 243 <param name="model_opt_precision" argument="-e" type="float" label="Model optimization precision" value="" optional="true"
292 help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used (--model_opt_precision)" optional="True" /> 244 help="Set model optimization precision in log likelihood units for final optimization of tree topology" />
293 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" help="(-E)" /> 245 <param name="excludefile" argument="-E" type="data" format="txt" optional="true" label="Exclude file" help="Should contain a specification of alignment positions you wish to exclude" />
294 <param name="search_algorithm" type="select" label="Algorithm to execute" help="(-f)" optional="True"> 246 <param name="search_algorithm" argument="-f" type="select" label="Algorithm to execute" optional="true">
295 <option value="a">Rapid bootstrap and best ML tree search (a)</option> 247 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
296 <option value="A">Compute marginal ancestral states (A)</option> 248 <option value="A">Compute marginal ancestral states (A)</option>
297 <option value="b">Draw bipartition information (b)</option> 249 <option value="b">Draw bipartition information (b)</option>
298 <option value="c">Check if the alignment can be read (c)</option> 250 <option value="c">Check if the alignment can be read (c)</option>
299 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option> 251 <option value="d" selected="true">New rapid hill-climbing (d)</option>
300 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option> 252 <option value="D">Rapid hill-climbing with RELL bootstraps (D)</option>
253 <option value="e">Optimize model+branch lengths under GAMMA/GAMMAI only (e)</option>
301 <option value="g">Compute per-site log likelihoods for -z trees (g)</option> 254 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
302 <option value="h">Compute log likelihood test for -t / -z trees (h)</option> 255 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
303 <option value="j">Generate bootstrapped alignment files (j)</option> 256 <option value="j">Generate bootstrapped alignment files (j)</option>
304 <option value="J">Compute SH-like support values for the -t tree (J)</option> 257 <option value="J">Compute SH-like support values for the -t tree (J)</option>
305 <option value="m">Compare bipartitions between -t and -z trees (m)</option> 258 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
316 <option value="v">Classify environmental sequences (v)</option> 269 <option value="v">Classify environmental sequences (v)</option>
317 <option value="w">Compute ELW-test on -z trees (w)</option> 270 <option value="w">Compute ELW-test on -z trees (w)</option>
318 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option> 271 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
319 <option value="y">Classify environmental sequences into a reference tree (y)</option> 272 <option value="y">Classify environmental sequences into a reference tree (y)</option>
320 </param> 273 </param>
321 <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="--save_memory_cat_model" falsevalue="" 274 <param name="save_memory_cat_model" argument="-F" type="boolean" truevalue="-F" falsevalue=""
322 display="checkboxes" label="ML tree searches under CAT model" optional="True" 275 label="ML tree searches under CAT model"
323 help="ML tree searches under CAT model for very large trees without switching to GAMMA in the end (saves memory) and no thorough optimization under GAMMA (--save_memory_cat_model)" /> 276 help="ML tree searches under CAT model for very large trees without switching to GAMMA in the end (saves memory) and no thorough optimization under GAMMA" />
324 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" help="(-g)" /> 277 <param name="groupingfile" argument="-g" type="data" format="txt" optional="true" label="Multifurcating constraint tree" help="This tree does not need to be comprehensive, i.e. does not have to contain all taxa" />
325 <param name="enable_evol_heuristics" type="float" label="Enable the ML-based evolutionary placement algorithm heuristics" 278 <param name="enable_evol_heuristics" argument="-G" type="float" min="0.0" max="1.0" optional="true"
326 help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML). (--enable_evol_heuristics)" optional="True" > 279 label="Enable the ML-based evolutionary placement algorithm heuristics"
327 <validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/> 280 help="By specifying a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)" />
328 </param> 281 <param name="initial_rearrangement_setting" argument="-i" type="integer" value="" optional="true" label="Initial rearrangement setting for the subsequent application of topological changes phase" />
329 <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" help="(-i)"/> 282 <param name="posterior_bootstopping_analysis" argument="-I" type="select" optional="true" label="A posteriori bootstopping analysis">
330 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True" help="(-I)">
331 <option value="" selected="True"></option>
332 <option value="autoFC">Frequency-based criterion (autoFC)</option> 283 <option value="autoFC">Frequency-based criterion (autoFC)</option>
333 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option> 284 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
334 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option> 285 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
335 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option> 286 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
336 </param> 287 </param>
337 <!-- (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy --> 288 <!-- (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy -->
338 <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True" help="(-J)"> 289 <param name="majority_rule_consensus" argument="-J" type="select" optional="true" label="Compute consensus tree">
339 <option value="" selected="True"></option>
340 <option value="MR">Majority-rule consensus tree (MR)</option> 290 <option value="MR">Majority-rule consensus tree (MR)</option>
341 <option value="MRE">Extended majority-rule consensus tree (MRE)</option> 291 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
342 <option value="STRICT">Strict consensus tree (STRICT)</option> 292 <option value="STRICT">Strict consensus tree (STRICT)</option>
343 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option> 293 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
344 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option> 294 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
345 </param> 295 </param>
346 <param name="print_branch_lengths" type="boolean" checked="no" truevalue="--print_branch_lengths" falsevalue="" display="checkboxes" label="Print bootstrapped trees with branch lengths" help="Specifies that bootstrapped trees should be printed with branch lengths. The bootstraps will run a bit longer, because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively. (-k)" optional="True" /> 296 <param name="print_branch_lengths" argument="-k" type="boolean" truevalue="-k" falsevalue=""
347 <param name="multistate_sub_model" type="select" optional="True" label="Specify a multi-state substitution model" help="(-K)"> 297 label="Print bootstrapped trees with branch lengths"
348 <option value="" selected="true"></option> 298 help="The bootstraps will run a bit longer, because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively" />
349 <option value="GTR">GTR</option> 299 <param name="multistate_sub_model" argument="-K" type="select" label="Specify a multi-state substitution model">
300 <option value="GTR" selected="true">GTR</option>
350 <option value="ORDERED">ORDERED</option> 301 <option value="ORDERED">ORDERED</option>
351 <option value="MK">MK</option> 302 <option value="MK">MK</option>
352 </param> 303 </param>
353 <param name="estimate_individual_branch_lengths" type="boolean" checked="no" 304 <param name="estimate_individual_branch_lengths" argument="-M" type="boolean" truevalue="-M" falsevalue=""
354 truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes" 305 label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file. A weighted average of the branch lengths is computed by using the respective partition lengths" />
355 label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-M)." optional="True" /> 306 <param name="outgroup_name" argument="-o" type="text" value="" optional="true" label="Outgroup name"
356 <param name="outgroup_name" type="text" value="" label="Outgroup name" 307 help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed" />
357 help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed. (-o)" optional="True" /> 308 <param name="disable_undetermined_seq_check" argument="-O" type="boolean" truevalue="-O" falsevalue=""
358 <param name="disable_undetermined_seq_check" type="boolean" checked="no" 309 label="Disable check for completely undetermined sequence in alignment"
359 truevalue="--disable_undertermined_seq_check" falsevalue="" display="checkboxes" label="Disable check for completely undetermined sequence in alignment" optional="True" help="Disable the check for completely undetermined sequence in alignment. The program will not exit with an error message when '-O' is specified." /> 310 help="The program will not exit with an error message when '-O' is specified." />
360 <param name="external_protein_model" format="txt" type="data" label="External AA substitution model" 311 <param name="external_protein_model" argument="-P" type="data" format="txt" optional="true" label="External AA (Protein) substitution model"
361 help="Specify the file name of a user-defined AA (Protein) substitution model. This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies. (--external_protein_model)" optional="True" /> 312 help="This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies" />
362 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" 313 <param name="multiple_model" argument="-q" type="data" format="txt" optional="true"
363 help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual. (--multiple_model)" /> 314 label="Assignment of models to alignment partitions for multiple models of substitution"
364 <param name="constraint_file" format="txt" type="data" label="Binary constraint tree" optional="True" 315 help="For the syntax of this file please consult the RaXML manual" />
365 help="Specify the file name of a binary constraint tree. This tree does not need to be comprehensive, i.e. must not contain all taxa. (--constrain_file)" /> 316 <param name="constraint_file" argument="-r" type="data" format="txt" optional="true" label="Binary constraint tree"
366 <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" optional="True" 317 help="This tree does not need to be comprehensive, i.e. does not have to contain all taxa" />
367 help="Specify the file name of a binary model parameter file that has previously been generated with RAxML using the '-f e' tree evaluation option. (-R)" /> 318 <param name="bin_model_parameter_file" argument="-R" type="data" format="txt" optional="true" label="Binary model parameter file"
368 <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" optional="True" 319 help="This parameter file can be generated with RAxML using the '-f e' tree evaluation option" />
369 help="Specify the name of a secondary structure file. The file can contain '.' for alignment columns that do not form part of a stem and characters '()&lt;&gt;[]{}' to define stem regions and pseudoknots. (-S)"/> 320 <param name="secondary_structure_file" argument="-S" type="data" format="txt" optional="true" label="Secondary structure file"
370 <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True" 321 help="The file can contain '.' for alignment columns that do not form part of a stem and characters '()&lt;&gt;[]{}' to define stem regions and pseudoknots" />
371 help="Specify a user starting tree file name in Newick format. (-t)" /> 322 <param name="start_tree_file" argument="-t" type="data" format="nhx" optional="true" label="Starting tree file" help="In Newick format" />
372 <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation" 323 <param name="use_median_approximation" argument="-u" type="boolean" truevalue="-u" falsevalue=""
373 help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity. (-T)" optional="True" /> 324 label="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity" />
374 <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="--save_memory_gappy_alignments" falsevalue="" display="checkboxes" label="Save memory on large gappy alignments" 325 <param name="save_memory_gappy_alignments" argument="-U" type="boolean" truevalue="-U" falsevalue=""
375 help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments. (-U)" optional="True" /> 326 label="Save memory on large gappy alignments"
376 <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="--disable_raite_heterogeneity" falsevalue="" display="checkboxes" label="Disable rate heterogeneity" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity. (_V)" optional="True" /> 327 help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments. This will only work for DNA and/or PROTEIN data" />
377 <param name="sliding_window_size" type="integer" value="" label="Sliding window size" optional="True" 328 <param name="disable_rate_heterogeneity" argument="-V" type="boolean" truevalue="-V" falsevalue=""
378 help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites' (-W)" /> 329 label="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead"
379 <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes" 330 help="Only works if you specify the CAT model of rate heterogeneity" />
380 label="Compute a randomized parsimony starting tree only" optional="True" 331 <param name="sliding_window_size" argument="-W" type="integer" min="1" value="100"
381 help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." /> 332 label="Sliding window size for leave-one-out site-specific placement bias algorithm"
382 <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file" 333 help="Only effective when used in combination with '-f S'" />
383 help="Specify the file name of a file containing multiple trees e.g. from a bootstrap that shall be used to draw bipartition values onto a tree provided with '-t', It can also be used to compute per site log likelihoods in combination with '-f g' and to read a bunch of trees for '-f h', '-f m' and '-f n'. (-z)" optional="True" /> 334 <param name="parsimony_starting_tree_only" argument="-y" type="boolean" truevalue="-y" falsevalue=""
384 <param name="random_seed" type="integer" value="1234567890" label="Random 335 label="Compute a randomized parsimony starting tree only"
385 seed used for the parsimony inferences" help="(--random_seed)"/> 336 help="The program will exit after computation of the starting tree" />
386 </when> 337 </when>
387 </conditional> 338 </conditional>
388 </inputs> 339 </inputs>
389 <outputs> 340 <outputs>
390 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" /> 341 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
391 <!-- REQUIRED --> 342 <!-- REQUIRED -->
392 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log"> 343 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
393 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> 344 <filter>selExtraOpts['extraOptions'] == 'required'</filter>
394 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> 345 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
395 </data> 346 </data>
396 <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> 347 <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
397 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> 348 <filter>selExtraOpts['extraOptions'] == 'required'</filter>
398 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> 349 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
399 </data> 350 </data>
400 <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result"> 351 <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
401 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> 352 <filter>selExtraOpts['extraOptions'] == 'required'</filter>
402 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> 353 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
403 </data> 354 </data>
404 <!-- ADVANCED --> 355 <!-- ADVANCED -->
405 <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree"> 356 <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
406 <filter>selExtraOpts['search_complete_random_tree'] is True</filter> 357 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
407 <filter>selExtraOpts['extraOptions'] == "full"</filter> 358 <filter>selExtraOpts['extraOptions'] == "full"</filter>
408 </data> 359 </data>
409 <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> 360 <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
410 <!-- <filter>(selExtraOpts['extraOptions'] == 'full')</filter> --> 361 <!-- <filter>selExtraOpts['extraOptions'] == 'full'</filter> -->
411 <!-- <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> 362 <!-- <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
412 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter> --> 363 <filter>not selExtraOpts['majority_rule_consensus']</filter> -->
413 </data> 364 </data>
414 <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> 365 <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
415 <filter>(selExtraOpts['extraOptions'] == "full")</filter> 366 <filter>selExtraOpts['extraOptions'] == "full"</filter>
416 <filter>(selExtraOpts['multiple_model'] != '')</filter> 367 <filter>selExtraOpts['multiple_model'] != ''</filter>
417 </data> 368 </data>
418 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions"> 369 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
419 <filter>(selExtraOpts['extraOptions'] == "full")</filter> 370 <filter>selExtraOpts['extraOptions'] == "full"</filter>
420 <filter>selExtraOpts['multiple_model'] is not None </filter> 371 <filter>selExtraOpts['multiple_model'] is not None </filter>
421 </data> 372 </data>
422 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log"> 373 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
423 <filter>(selExtraOpts['extraOptions'] == "full")</filter> 374 <filter>selExtraOpts['extraOptions'] == "full"</filter>
424 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> 375 <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
425 <filter>(selExtraOpts['bootseed'] == '')</filter> 376 <filter>selExtraOpts['bootseed'] == ''</filter>
426 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> 377 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
427 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> 378 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
428 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> 379 <filter>not selExtraOpts['majority_rule_consensus']</filter>
429 </data> 380 </data>
430 <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result"> 381 <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
431 <filter>(selExtraOpts['extraOptions'] == "full")</filter> 382 <filter>selExtraOpts['extraOptions'] == "full"</filter>
432 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> 383 <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
433 <filter>selExtraOpts['bootseed'] == ''</filter> 384 <filter>selExtraOpts['bootseed'] == ''</filter>
434 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> 385 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
435 <filter>selExtraOpts['search_algorithm'] != 'b'</filter> 386 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
436 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> 387 <filter>not selExtraOpts['majority_rule_consensus']</filter>
437 </data> 388 </data>
438 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions"> 389 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
439 <filter>(selExtraOpts['extraOptions'] == "full")</filter> 390 <filter>selExtraOpts['extraOptions'] == "full"</filter>
440 <filter>(selExtraOpts['multiple_model'] is not None)</filter> 391 <filter>selExtraOpts['multiple_model'] is not None</filter>
441 </data> 392 </data>
442 <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> 393 <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
443 <filter>(selExtraOpts['extraOptions'] == "full")</filter> 394 <filter>selExtraOpts['extraOptions'] == "full"</filter>
444 <!-- 395 <!--
445 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> 396 <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
446 <filter>(selExtraOpts['bootseed'] == '')</filter> 397 <filter>selExtraOpts['bootseed'] == ''</filter>
447 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> 398 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
448 <filter>(selExtraOpts['constraint_file'] is None)</filter> 399 <filter>selExtraOpts['constraint_file'] is None</filter>
449 <filter>(selExtraOpts['groupingfile'] is None)</filter> 400 <filter>selExtraOpts['groupingfile'] is None</filter>
450 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter> 401 <filter>selExtraOpts['search_complete_random_tree'] is False</filter>
451 <filter>(selExtraOpts['start_tree_file'] is None)</filter> 402 <filter>selExtraOpts['start_tree_file'] is None</filter>
452 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> 403 <filter>not selExtraOpts['majority_rule_consensus'] == ''</filter>
453 --> 404 -->
454 </data> 405 </data>
455 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees"> 406 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
456 <filter>selExtraOpts['extraOptions'] == "full"</filter> 407 <filter>selExtraOpts['extraOptions'] == "full"</filter>
457 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter> 408 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
458 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter> 409 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
459 </data> 410 </data>
460 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions"> 411 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
461 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> 412 <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
462 <filter>selExtraOpts['extraOptions'] == "full"</filter> 413 <filter>selExtraOpts['extraOptions'] == "full"</filter>
463 </data> 414 </data>
464 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels"> 415 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
465 <filter>selExtraOpts['extraOptions'] == "full"</filter> 416 <filter>selExtraOpts['extraOptions'] == "full"</filter>
466 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> 417 <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
467 </data> 418 </data>
468 <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree"> 419 <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
469 <filter>selExtraOpts['extraOptions'] == "full"</filter> 420 <filter>selExtraOpts['extraOptions'] == "full"</filter>
470 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter> 421 <filter>selExtraOpts['majority_rule_consensus'] == 'STRICT'</filter>
471 </data> 422 </data>
472 <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree"> 423 <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
473 <filter>selExtraOpts['extraOptions'] == "full"</filter> 424 <filter>selExtraOpts['extraOptions'] == "full"</filter>
474 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter> 425 <filter>selExtraOpts['majority_rule_consensus'] == 'MR'</filter>
475 </data> 426 </data>
476 <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree"> 427 <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
477 <filter>selExtraOpts['extraOptions'] == "full"</filter> 428 <filter>selExtraOpts['extraOptions'] == "full"</filter>
478 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter> 429 <filter>selExtraOpts['majority_rule_consensus'] == 'MRE'</filter>
479 </data> 430 </data>
480 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences."> 431 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
481 <filter>selExtraOpts['search_algorithm'] == 'm' </filter> 432 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
482 <filter>selExtraOpts['extraOptions'] == "full"</filter> 433 <filter>selExtraOpts['extraOptions'] == "full"</filter>
483 </data> 434 </data>
521 <has_text_matching expression="Whale" /> 472 <has_text_matching expression="Whale" />
522 </assert_contents> 473 </assert_contents>
523 </output> 474 </output>
524 </test> 475 </test>
525 </tests> 476 </tests>
526 <help> 477 <help><![CDATA[
527
528 RAxML_ (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic 478 RAxML_ (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic
529 trees. The program is explicitly being developed to efficiently infer trees for 479 trees. The program is explicitly being developed to efficiently infer trees for
530 extremely large datasets, either in terms of the number of taxa and/or the 480 extremely large datasets, either in terms of the number of taxa and/or the
531 sequence length. 481 sequence length.
532 482
533 483 .. _RAxML: http://www.exelixis-lab.org/web/software/raxml/
534 .. _RAxML: http://www.exelixis-lab.org/
535
536 484
537 **Tool development**: 485 **Tool development**:
538 486
539 Oleksandr Moskalenko with adaptations from Tiago Antao. 487 Oleksandr Moskalenko with adaptations from Tiago Antao.
540 488 ]]></help>
541 </help>
542 <citations> 489 <citations>
543 <citation type="doi">10.1093/bioinformatics/btu033</citation> 490 <citation type="doi">10.1093/bioinformatics/btu033</citation>
544 </citations> 491 </citations>
545 </tool> 492 </tool>