|
0
|
1 <tool id="raxml" name="RaXML BETA (Testing)" version="1.0.0">
|
|
|
2 <requirements><requirement type='package'>raxml</requirement></requirements>
|
|
|
3 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
|
|
|
4 <command interpreter="python">raxml.py
|
|
|
5 ## Required parameters
|
|
|
6 ## Program name and threads are hard-coded as they are dependent on the binary and threads are specified in the Galaxy's tool configuration
|
|
|
7 ## binary is hard-coded to the pthreads enabled raxml executable
|
|
|
8 --binary "raxmlHPC-PTHREADS-SSE3"
|
|
|
9 ## (-T)
|
|
|
10 --threads 4
|
|
|
11 ## (-s)
|
|
|
12 --source $infile
|
|
|
13 ## (-m)
|
|
|
14 --model_type $search_model_selector.model_type
|
|
|
15 --base_model $search_model_selector.base_model
|
|
|
16 #if str( $search_model_selector.model_type ) == 'aminoacid':
|
|
|
17 #if str( $search_model_selector.aa_model_empirical_base_frequences) == 'true':
|
|
|
18 --aa_empirical_freq
|
|
|
19 #end if
|
|
|
20 #if $search_model_selector.aa_search_matrix:
|
|
|
21 --aa_search_matrix $search_model_selector.aa_search_matrix
|
|
|
22 #end if
|
|
|
23 #end if
|
|
|
24 ## (-p)
|
|
|
25 #if $random_seed:
|
|
|
26 --random_seed $random_seed
|
|
|
27 #else
|
|
|
28 --random_seed 1234567890
|
|
|
29 #end if
|
|
|
30
|
|
|
31 ## Optional parameters
|
|
|
32
|
|
|
33 #if str( $selExtraOpts.extraOptions ) == 'full':
|
|
|
34 ## (-N/#)
|
|
|
35 #if $selExtraOpts.number_of_runs:
|
|
|
36 --number_of_runs $selExtraOpts.number_of_runs
|
|
|
37 #end if
|
|
|
38 #if $selExtraOpts.number_of_runs_bootstop:
|
|
|
39 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop
|
|
|
40 #end if
|
|
|
41 ## (-a)
|
|
|
42 #if $selExtraOpts.weightfile:
|
|
|
43 --weightfile $selExtraOpts.weightfile
|
|
|
44 #end if
|
|
|
45 ## (-b)
|
|
|
46 #if str ($selExtraOpts.secondary_structure_model) != "":
|
|
|
47 --secondary_structure_model $selExtraOpts.secondary_structure_model
|
|
|
48 #end if
|
|
|
49 ## (-b)
|
|
|
50 #if $selExtraOpts.bootseed:
|
|
|
51 --bootseed $selExtraOpts.bootseed
|
|
|
52 #end if
|
|
|
53 ## (-c)
|
|
|
54 #if $selExtraOpts.numofcats:
|
|
|
55 --numofcats $selExtraOpts.numofcats
|
|
|
56 #end if
|
|
|
57 ## (-d)
|
|
|
58 #if str ($selExtraOpts.search_complete_random_tree) == "true":
|
|
|
59 --search_complete_random_tree
|
|
|
60 #end if
|
|
|
61 ## (-D)
|
|
|
62 #if str ($selExtraOpts.ml_search_convergence) == "true":
|
|
|
63 --ml_search_convergence
|
|
|
64 #end if
|
|
|
65 ## (-e)
|
|
|
66 #if $selExtraOpts.model_opt_precision:
|
|
|
67 --model_opt_precision $selExtraOpts.model_opt_precision
|
|
|
68 #end if
|
|
|
69 ## (-E)
|
|
|
70 #if $selExtraOpts.excludefile:
|
|
|
71 --excludefile $selExtraOpts.excludefile
|
|
|
72 #end if
|
|
|
73 ## (-f)
|
|
|
74 #if $selExtraOpts.search_algorithm:
|
|
|
75 --search_algorithm $selExtraOpts.search_algorithm
|
|
|
76 #end if
|
|
|
77 ## (-F)
|
|
|
78 #if str ($selExtraOpts.save_memory_cat_model) == "true":
|
|
|
79 --save_memory_cat_model
|
|
|
80 #end if
|
|
|
81 ## (-g)
|
|
|
82 #if $selExtraOpts.groupingfile:
|
|
|
83 --groupingfile $selExtraOpts.groupingfile
|
|
|
84 #end if
|
|
|
85 ## (-G)
|
|
|
86 #if $selExtraOpts.enable_evol_heuristics:
|
|
|
87 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics
|
|
|
88 #end if
|
|
|
89 ## (-i)
|
|
|
90 #if $selExtraOpts.initial_rearrangement_setting:
|
|
|
91 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting
|
|
|
92 #end if
|
|
|
93 ## (-I)
|
|
|
94 #if $selExtraOpts.posterior_bootstopping_analysis:
|
|
|
95 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis
|
|
|
96 #end if
|
|
|
97 ## (-J)
|
|
|
98 #if $selExtraOpts.majority_rule_consensus:
|
|
|
99 --majority_rule_consensus $selExtraOpts.majority_rule_consensus
|
|
|
100 #end if
|
|
|
101 ## (-k)
|
|
|
102 #if str ($selExtraOpts.print_branch_lengths) == "true":
|
|
|
103 --print_branch_lengths
|
|
|
104 #end if
|
|
|
105 ## (-K)
|
|
|
106 #if str ($selExtraOpts.multistate_sub_model) != "":
|
|
|
107 --multistate_sub_model $selExtraOpts.multistate_sub_model
|
|
|
108 #end if
|
|
|
109 ## (-m) - see elsewhere
|
|
|
110 ## (-M)
|
|
|
111 #if str ($selExtraOpts.estimate_individual_branch_lengths) == "true":
|
|
|
112 --estimate_individual_branch_lengths
|
|
|
113 #end if
|
|
|
114 ## (-n) - see elsewhere
|
|
|
115 ## (-o)
|
|
|
116 #if $selExtraOpts.outgroup_name:
|
|
|
117 --outgroup_name $selExtraOpts.outgroup_name
|
|
|
118 #end if
|
|
|
119 ## (-O)
|
|
|
120 #if str ($selExtraOpts.disable_undetermined_seq_check) == "true":
|
|
|
121 --disable_undetermined_seq_check
|
|
|
122 #end if
|
|
|
123 ## (-P)
|
|
|
124 #if $selExtraOpts.external_protein_model:
|
|
|
125 --external_protein_model $selExtraOpts.external_protein_model
|
|
|
126 #end if
|
|
|
127 ## (-q)
|
|
|
128 #if $selExtraOpts.multiple_model:
|
|
|
129 --multiple_model $selExtraOpts.multiple_model
|
|
|
130 #end if
|
|
|
131 ## (-r)
|
|
|
132 #if $selExtraOpts.constraint_file:
|
|
|
133 --constraint_file $selExtraOpts.constraint_file
|
|
|
134 #end if
|
|
|
135 ## (-R)
|
|
|
136 #if $selExtraOpts.bin_model_parameter_file:
|
|
|
137 --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file
|
|
|
138 #end if
|
|
|
139 ## (-S)
|
|
|
140 #if $selExtraOpts.secondary_structure_file:
|
|
|
141 --secondary_structure_file $selExtraOpts.secondary_structure_file
|
|
|
142 #end if
|
|
|
143 ## (-t)
|
|
|
144 #if $selExtraOpts.start_tree_file:
|
|
|
145 --starting_tree $selExtraOpts.start_tree_file
|
|
|
146 #end if
|
|
|
147 ## (-T) see elsewhere
|
|
|
148 ## (-u)
|
|
|
149 #if str ($selExtraOpts.use_median_approximation) == "true":
|
|
|
150 --use_median_approximation
|
|
|
151 #end if
|
|
|
152 ## (-U)
|
|
|
153 #if str ($selExtraOpts.save_memory_gappy_alignments) == "true":
|
|
|
154 --save_memory_gappy_alignments
|
|
|
155 #end if
|
|
|
156 ## (-V)
|
|
|
157 #if str ($selExtraOpts.disable_rate_heterogeneity) == "true":
|
|
|
158 --disable_rate_heterogeneity
|
|
|
159 #end if
|
|
|
160 ## (-W)
|
|
|
161 #if $selExtraOpts.sliding_window_size:
|
|
|
162 --sliding_window_size $selExtraOpts.sliding_window_size
|
|
|
163 #end if
|
|
|
164 ## (-x)
|
|
|
165 #if $selExtraOpts.rapid_bootstrap_random_seed:
|
|
|
166 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
|
|
|
167 #end if
|
|
|
168 ## (-y)
|
|
|
169 #if str ($selExtraOpts.parsimony_starting_tree_only) == "true":
|
|
|
170 --parsimony_starting_tree_only
|
|
|
171 #end if
|
|
|
172 ## (-z)
|
|
|
173 #if $selExtraOpts.file_multiple_trees:
|
|
|
174 --file_multiple_trees $selExtraOpts.file_multiple_trees
|
|
|
175 #end if
|
|
|
176 #end if
|
|
|
177
|
|
|
178 ##silent sys.stderr.write("DEBUG1 START\n")
|
|
|
179 ##silent sys.stderr.write($selExtraOpts.extraOptions)
|
|
|
180 ##silent sys.stderr.write("\nDEBUG1 END\n")
|
|
|
181
|
|
|
182 </command>
|
|
|
183 <inputs>
|
|
|
184 ## (-m)
|
|
|
185 <conditional name="search_model_selector">
|
|
|
186 <param name="model_type" type="select" label="Model Type">
|
|
|
187 <option value="nucleotide" selected="true">Nucleotide</option>
|
|
|
188 <option value="aminoacid">Amino Acid</option>
|
|
|
189 <option value="binary">Binary</option>
|
|
|
190 <option value="multistate">Multistate</option>
|
|
|
191 </param>
|
|
|
192 <when value="nucleotide">
|
|
|
193 ## Nucleotide substitution models
|
|
|
194 <param name="base_model" type="select" label="Substitution Model (-m)">
|
|
|
195 <option value="GTRCAT">GTRCAT</option>
|
|
|
196 <option value="GTRCATI">GTRCATI</option>
|
|
|
197 <option value="GTRGAMMA" select="true">GTRGAMMA</option>
|
|
|
198 <option value="GTRGAMMAI">GTRGAMMAI</option>
|
|
|
199 </param>
|
|
|
200 </when>
|
|
|
201 ## Aminoacid substitution models
|
|
|
202 <when value="aminoacid">
|
|
|
203 <param name="aa_model_empirical_base_frequences"
|
|
|
204 type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use empirical base frequencies in AA models" />
|
|
|
205 <param name="base_model" type="select" label="Substitution Model (-m)">
|
|
|
206 <option value="PROTCAT" select="true">PROTCAT</option>
|
|
|
207 <option value="PROTCATI">PROTCATI</option>
|
|
|
208 <option value="PROTGAMMA">PROTGAMMA</option>
|
|
|
209 <option value="PROTGAMMAI">PROTGAMMAI</option>
|
|
|
210 </param>
|
|
|
211 <param name="aa_search_matrix" type="select" label="Matrix">
|
|
|
212 <option value="DAYHOFF" select="true">DAYHOFF</option>
|
|
|
213 <option value="DCMUT">DCMUT</option>
|
|
|
214 <option value="JTT">JTT</option>
|
|
|
215 <option value="MTREV">MTREV</option>
|
|
|
216 <option value="WAG">WAG</option>
|
|
|
217 <option value="RTREV">RTREV</option>
|
|
|
218 <option value="CPREV">CPREV</option>
|
|
|
219 <option value="VT">VT</option>
|
|
|
220 <option value="BLOSUM62">BLOSUM62</option>
|
|
|
221 <option value="MTMAM">MTMAM</option>
|
|
|
222 <option value="LG">LG</option>
|
|
|
223 <option value="MTART">MTART</option>
|
|
|
224 <option value="MTZOA">MTZOA</option>
|
|
|
225 <option value="PMB">PMB</option>
|
|
|
226 <option value="HIVB">HIVB</option>
|
|
|
227 <option value="HIVW">HIVW</option>
|
|
|
228 <option value="JTTDCMUT">JTTDCMUT</option>
|
|
|
229 <option value="FLU">FLU</option>
|
|
|
230 <option value="DUMMY">DUMMY</option>
|
|
|
231 <option value="DUMMY2">DUMMY2</option>
|
|
|
232 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
|
|
|
233 <option value="GTR">GTR</option>
|
|
|
234 </param>
|
|
|
235 </when>
|
|
|
236 ## Binary substitution models
|
|
|
237 <when value="binary">
|
|
|
238 <param name="base_model" type="select" label="Substitution Model (-m)">
|
|
|
239 <option value="BINCAT">BINCAT</option>
|
|
|
240 <option value="BINCATI">BINCATI</option>
|
|
|
241 <option value="BINGAMMA">BINGAMMA</option>
|
|
|
242 <option value="BINGAMMAI">BINGAMMAI</option>
|
|
|
243 </param>
|
|
|
244 </when>
|
|
|
245 ## Multi-state substitution models
|
|
|
246 <when value="multistate">
|
|
|
247 <param name="base_model" type="select" label="Substitution Model (-m)">
|
|
|
248 <option value="MULTICAT">MULTICAT</option>
|
|
|
249 <option value="MULTICATI">MULTICATI</option>
|
|
|
250 <option value="MULTIGAMMA">MULTIGAMMA</option>
|
|
|
251 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
|
|
|
252 </param>
|
|
|
253 </when>
|
|
|
254 </conditional>
|
|
|
255 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random
|
|
|
256 seed used for the parsimony inferences (-p)" />
|
|
|
257 <conditional name="selExtraOpts">
|
|
|
258 <param name="extraOptions" type="select" label="RAxML options to use"
|
|
|
259 help="The required minimal settings are the input file and the
|
|
|
260 substitution model. To specify extra options select the 'Full option list'">
|
|
|
261 <option value="required">Required options only</option>
|
|
|
262 <option value="full">Full option list</option>
|
|
|
263 </param>
|
|
|
264 <when value="required">
|
|
|
265 ## (-s)
|
|
|
266 <param name="infile" format="txt" type="data" label="Sequence File (relaxed PHYLIP format) (-s)"/>
|
|
|
267 </when>
|
|
|
268 <when value="full">
|
|
|
269 ## (-s)
|
|
|
270 <param name="infile" format="txt" type="data" label="Sequence File (relaxed PHYLIP format) (-s)" optional="True"/>
|
|
|
271 ## (-N/#)
|
|
|
272 <param name="number_of_runs" type="integer" size="8" value=""
|
|
|
273 label="Number of runs (-N|#)" help="Specify the number of
|
|
|
274 alternative runs on distinct starting trees In combination
|
|
|
275 with the '-b' option will invoke a multiple boostrap analysis.
|
|
|
276 You can add the bootstopping criteria by choosing the autoMR,
|
|
|
277 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
|
|
|
278 providing a number here. Bootstopping will only work in
|
|
|
279 combination with '-x' or '-b'."
|
|
|
280 optional="True" />
|
|
|
281 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs (-N/#)" optional="True">
|
|
|
282 <option value="" selected="yes"></option>
|
|
|
283 <option value="autoMR">autoMR</option>
|
|
|
284 <option value="autoMRE">autoMRE</option>
|
|
|
285 <option value="autoMRE_IGN">autoMRE_IGN</option>
|
|
|
286 <option value="autoFC">autoFC</option>
|
|
|
287 </param>
|
|
|
288 ## Alphabetical Listing of Advanced Options
|
|
|
289 ## (-a)
|
|
|
290 <param format="txt" name="weightfile" type="data" label="Column weight file (-a)" optional="True" />
|
|
|
291 ## (-A)
|
|
|
292 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model (-A)" optional="True">
|
|
|
293 <option value="" selected="yes"></option>
|
|
|
294 <option value="S6A">S6A</option>
|
|
|
295 <option value="S6B">S6B</option>
|
|
|
296 <option value="S6C">S6C</option>
|
|
|
297 <option value="S6D">S6D</option>
|
|
|
298 <option value="S6E">S6E</option>
|
|
|
299 <option value="S7A">S7A</option>
|
|
|
300 <option value="S7B">S7B</option>
|
|
|
301 <option value="S7C">S7C</option>
|
|
|
302 <option value="S7D">S7D</option>
|
|
|
303 <option value="S7E">S7E</option>
|
|
|
304 <option value="S7F">S7F</option>
|
|
|
305 <option value="S16">S16</option>
|
|
|
306 <option value="S16A">S16A</option>
|
|
|
307 <option value="S16B">S16B</option>
|
|
|
308 </param>
|
|
|
309 ## (-b)
|
|
|
310 <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping (-b)" refresh_on_change='true' optional="True" />
|
|
|
311 ## (-x)
|
|
|
312 <param name="rapid_bootstrap_random_seed" type="integer" value='' size="7" label="Rapid bootstrapping random seed (-x)" optional="True" 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." />
|
|
|
313 ## (-B)
|
|
|
314 <param name="cutoff_threshold" type="float" size="8" label="MR Cutoff threshold (-B)" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" />
|
|
|
315 ## (-c)
|
|
|
316 <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX (-c)" optional="True" />
|
|
|
317 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now.
|
|
|
318 ## (-d)
|
|
|
319 <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="true" falsevalue="false" display="checkboxes" label="Start ML optimization from a complete random starting tree (-d)" />
|
|
|
320 ## (-D)
|
|
|
321 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="true" falsevalue="false" label="ML search convergence criterion (-D)" />
|
|
|
322 ## (-e)
|
|
|
323 <param name="model_opt_precision" type="float" size="8" label="Model optimization precision (-e)" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" />
|
|
|
324 ## (-E)
|
|
|
325 <param format="txt" name="excludefile" type="data" label="Exclude file (-E)" optional="True" />
|
|
|
326 ## (-f)
|
|
|
327 <param name="search_algorithm" type="select" label="Algorithm to execute (-f)" optional="True">
|
|
|
328 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
|
|
|
329 <option value="A">Compute marginal ancestral states (A)</option>
|
|
|
330 <option value="b">Draw bipartition information (b)</option>
|
|
|
331 <option value="c">Check if the alignment can be read (c)</option>
|
|
|
332 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option>
|
|
|
333 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
|
|
|
334 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
|
|
|
335 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
|
|
|
336 <option value="j">Generate bootstrapped alignment files (j)</option>
|
|
|
337 <option value="J">Compute SH-like support values for the -t tree (J)</option>
|
|
|
338 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
|
|
|
339 <option value="n">Compute log likelihood score for -z trees (n)</option>
|
|
|
340 <option value="o">Use old slower search algorithm (o)</option>
|
|
|
341 <option value="p">Stepwise MP addition of new sequences (p)</option>
|
|
|
342 <option value="q">Fast quartet calculator (q)</option>
|
|
|
343 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
|
|
|
344 <option value="s">Split a multi-gene alignment (s)</option>
|
|
|
345 <option value="S">Compute site-specific placement bias (S)</option>
|
|
|
346 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
|
|
|
347 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
|
|
|
348 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
|
|
|
349 <option value="v">Classify environmental sequences (v)</option>
|
|
|
350 <option value="w">Compute ELW-test on -z trees (w)</option>
|
|
|
351 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
|
|
|
352 <option value="y">Classify environmental sequences into a reference tree (y)</option>
|
|
|
353 </param>
|
|
|
354 ## (-F)
|
|
|
355 <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="ML tree searches under CAT model (-F)" optional="True" 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" />
|
|
|
356 ## (-g)
|
|
|
357 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree (-g)" optional="True" />
|
|
|
358 ## (-G)
|
|
|
359 <param name="enable_evol_heuristics" type="float" size="8" label="Enable the ML-based evolutionary placement algorithm heuristics (-G)" 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)." optional="True" >
|
|
|
360 <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/>
|
|
|
361 </param>
|
|
|
362 ## (-i)
|
|
|
363 <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting (-i)" optional="True" />
|
|
|
364 ## (-I)
|
|
|
365 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis (-I)" optional="True">
|
|
|
366 <option value="" selected="True"></option>
|
|
|
367 <option value="autoFC">Frequency-based criterion (autoFC)</option>
|
|
|
368 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
|
|
|
369 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
|
|
|
370 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
|
|
|
371 </param>
|
|
|
372 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy
|
|
|
373 ## (-J)
|
|
|
374 <param name="majority_rule_consensus" type="select" label="Compute consensus tree (-J)" optional="True">
|
|
|
375 <option value="" selected="True"></option>
|
|
|
376 <option value="MR">Majority-rule consensus tree (MR)</option>
|
|
|
377 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
|
|
|
378 <option value="STRICT">Strict consensus tree (STRICT)</option>
|
|
|
379 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
|
|
|
380 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
|
|
|
381 </param>
|
|
|
382 ## (-k)
|
|
|
383 <param name="print_branch_lengths" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Print bootstrapped trees with branch lengths (-k)" 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." optional="True" />
|
|
|
384 ## (-K)
|
|
|
385 <param name="multistate_sub_model" type="select" label="Specify a
|
|
|
386 multi-state substitution model (-K)" optional="True">
|
|
|
387 <option value="" selected="true"></option>
|
|
|
388 <option value="GTR">GTR</option>
|
|
|
389 <option value="ORDERED">ORDERED</option>
|
|
|
390 <option value="MK">MK</option>
|
|
|
391 </param>
|
|
|
392 ## (-M)
|
|
|
393 <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Estimate individual per-partition branch lengths (-M)" help="Only has effect with a partition file (-q)." optional="True" />
|
|
|
394 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files
|
|
|
395 ## (-o)
|
|
|
396 <param name="outgroup_name" type="text" size="40" value="" label="Outgroup name (-o)" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" />
|
|
|
397 ## (-O)
|
|
|
398 <param name="disable_undetermined_seq_check" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Disable check for completely undetermined sequence in alignment (-O)" 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." />
|
|
|
399 <param name="external_protein_model" format="txt" type="data" label="External AA substitution model (-P)" 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." optional="True" />
|
|
|
400 ## (-q)
|
|
|
401 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions (-q)" optional="True" 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." />
|
|
|
402 ## (-r)
|
|
|
403 <param name="constraint_file" format="txt" type="data" label="Binary constraint tree (-r)" optional="True" 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." />
|
|
|
404 ## (-R)
|
|
|
405 <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file (-R)" optional="True" 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." />
|
|
|
406 ## (-s) source file option is in the required options section
|
|
|
407 ## (-S)
|
|
|
408 <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file (-S)" optional="True" 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 '()<>[]{}' to define stem regions and pseudoknots."/>
|
|
|
409 ## (-t)
|
|
|
410 <param name="start_tree_file" format="txt" type="data" label="Starting tree file (-t)" optional="True" help="Specify a user starting tree file name in Newick format." />
|
|
|
411 ## (-T) is hard-coded in the required options section
|
|
|
412 <param name="use_median_approximation" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use the median for the discrete approximation (-u)" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" />
|
|
|
413 ## (-U)
|
|
|
414 <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Save memory on large gappy alignments (-U)" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" />
|
|
|
415 ## (-V)
|
|
|
416 <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Disable rate heterogeneity (-V)" 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." optional="True" />
|
|
|
417 ## (-W)
|
|
|
418 <param name="sliding_window_size" type="integer" size="5" value="" label="Sliding window size (-W)" optional="True" 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'" />
|
|
|
419 ## (-x) - see it by the (-b)
|
|
|
420 ## (-y)
|
|
|
421 <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Compute a randomized parsimony starting tree only (-y)" optional="True" 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." />
|
|
|
422 ## (-z)
|
|
|
423 <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file (-z)" 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'." optional="True" />
|
|
|
424 </when> ## full option list
|
|
|
425 </conditional> ## END $selExtraOpts
|
|
|
426 </inputs>
|
|
|
427 <outputs>
|
|
|
428 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
|
|
|
429 ## REQUIRED
|
|
|
430 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
|
|
|
431 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
|
|
|
432 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
|
|
|
433 </data>
|
|
|
434 <data format="txt" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
|
|
|
435 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
|
|
|
436 </data>
|
|
|
437 <data format="txt" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
|
|
|
438 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
|
|
|
439 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
|
|
|
440 </data>
|
|
|
441 <data format="txt" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
|
|
|
442 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
|
|
|
443 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
|
|
|
444 </data>
|
|
|
445 ## ADVANCED
|
|
|
446 <data format="txt" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
|
|
|
447 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
|
|
|
448 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
449 </data>
|
|
|
450 <data format="txt" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
|
|
|
451 <filter>(selExtraOpts['extraOptions'] == 'full')</filter>
|
|
|
452 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '' or selExtraOpts['bootseed'] == '') and (selExtraOpts['search_algorithm'] == 'a')</filter>
|
|
|
453 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
|
|
|
454 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter>
|
|
|
455 </data>
|
|
|
456 <data format="txt" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
|
|
|
457 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
458 <filter>(selExtraOpts['multiple_model'] != '')</filter>
|
|
|
459 </data>
|
|
|
460 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
|
|
|
461 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
462 <filter>selExtraOpts['multiple_model'] is not None </filter>
|
|
|
463 </data>
|
|
|
464 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
|
|
|
465 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
466 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
|
|
|
467 <filter>(selExtraOpts['bootseed'] == '')</filter>
|
|
|
468 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
|
|
|
469 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
|
|
|
470 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
|
|
|
471 </data>
|
|
|
472 <data format="txt" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
|
|
|
473 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
474 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
|
|
|
475 <filter>selExtraOpts['bootseed'] == ''</filter>
|
|
|
476 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
|
|
|
477 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
|
|
|
478 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
|
|
|
479 </data>
|
|
|
480 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
|
|
|
481 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
482 <filter>(selExtraOpts['multiple_model'] is not None)</filter>
|
|
|
483 </data>
|
|
|
484 <data format="txt" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
|
|
|
485 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
|
|
|
486 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
|
|
|
487 <filter>(selExtraOpts['bootseed'] == '')</filter>
|
|
|
488 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
|
|
|
489 <filter>(selExtraOpts['constraint_file'] is None)</filter>
|
|
|
490 <filter>(selExtraOpts['groupingfile'] is None)</filter>
|
|
|
491 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter>
|
|
|
492 <filter>(selExtraOpts['start_tree_file'] is None)</filter>
|
|
|
493 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
|
|
|
494 </data>
|
|
|
495 <data format="txt" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
|
|
|
496 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
497 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
|
|
|
498 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
|
|
|
499 </data>
|
|
|
500 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
|
|
|
501 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
|
|
|
502 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
503 </data>
|
|
|
504 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
|
|
|
505 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
506 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
|
|
|
507 </data>
|
|
|
508 <data format="txt" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
|
|
|
509 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
510 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter>
|
|
|
511 </data>
|
|
|
512 <data format="txt" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
|
|
|
513 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
514 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter>
|
|
|
515 </data>
|
|
|
516 <data format="txt" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
|
|
|
517 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
518 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter>
|
|
|
519 </data>
|
|
|
520 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
|
|
|
521 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
|
|
|
522 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
523 </data>
|
|
|
524 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
|
|
|
525 <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
|
|
|
526 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
527 </data>
|
|
|
528 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
|
|
|
529 <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
|
|
|
530 <filter>selExtraOpts['extraOptions'] == "full"</filter>
|
|
|
531 </data>
|
|
|
532 </outputs>
|
|
|
533 <tests>
|
|
|
534 <test>
|
|
|
535 <!-- test1 -->
|
|
|
536 <!-- raxmlHPC-PTHREADS-SSE3 -T 4 -s raxml_binary.phy -n galaxy -m BINCAT -p 12345 -->
|
|
|
537 <param name="extraOptions" value="required"/>
|
|
|
538 <param name="infile" value="raxml/inputs/raxml_binary.phy"/>
|
|
|
539 <param name="model_type" value="binary"/>
|
|
|
540 <param name="base_model" value="BINCAT"/>
|
|
|
541 <output name="bestTreeReq" file="raxml/test1/RAxML_bestTree.galaxy"/>
|
|
|
542 <output name="parsimonyTreeReq" file="raxml/test1/RAxML_parsimonyTree.galaxy"/>
|
|
|
543 <!-- <output name="info" file="raxml/test1/RAxML_info.galaxy"/> -->
|
|
|
544 <output name="logReq" file="raxml/test1/RAxML_log.galaxy">
|
|
|
545 <assert_contents>
|
|
|
546 <has_line_matching expression="^0\\..*" />
|
|
|
547 </assert_contents>
|
|
|
548 </output>
|
|
|
549 <output name="resultReq" file="raxml/test1/RAxML_result.galaxy">
|
|
|
550 <assert_contents>
|
|
|
551 <has_line_matching expression="Overall\sexecution\stime.*" />
|
|
|
552 </assert_contents>
|
|
|
553 </output>
|
|
|
554 </test>
|
|
|
555 <!--
|
|
|
556 <test>
|
|
|
557 -->
|
|
|
558 <!-- test2 -->
|
|
|
559 <!-- raxmlHPC-PTHREADS-SSE3 -T 4 -s raxml_binary.phy -n galaxy -m BINCAT -p 12345 -->
|
|
|
560 <!--
|
|
|
561 <param name="infile" value="raxml/inputs/raxml_binary.phy"/>
|
|
|
562 <param name="search_model_selector" value="binary"/>
|
|
|
563 <param name="base_model" value="BINCAT"/>
|
|
|
564 <output name="info" file="raxml/test1/RAxML_info.galaxy"/>
|
|
|
565 <output name="logReq" file="raxml/test1/RAxML_log.galaxy"/>
|
|
|
566 <output name="bestTreeReq" file="raxml/test1/RAxML_bestTree.galaxy"/>
|
|
|
567 <output name="parsimonyTreeReq" file="raxml/test1/RAxML_parsimonyTree.galaxy"/>
|
|
|
568 <output name="resultReq" file="raxml/test1/RAxML_result.galaxy"/>
|
|
|
569 -->
|
|
|
570 <!--
|
|
|
571 </test>
|
|
|
572 -->
|
|
|
573 </tests>
|
|
|
574 <help>
|
|
|
575 Title:
|
|
|
576 ______
|
|
|
577 Randomized Axelerated Maximum Likelihood
|
|
|
578
|
|
|
579 Author:
|
|
|
580 _______
|
|
|
581 Alexandros Stamatakis <alexandros.stamatakis@h-its.org>
|
|
|
582
|
|
|
583 Description:
|
|
|
584 ____________
|
|
|
585
|
|
|
586 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic
|
|
|
587 trees. The program is explicitly being developed to efficiently infer trees for
|
|
|
588 extremely large datasets, either in terms of the number of taxa and/or the
|
|
|
589 sequence length.
|
|
|
590
|
|
|
591 This wrapper works with the RAxML version 7.3.2.
|
|
|
592
|
|
|
593 URL:
|
|
|
594 ____
|
|
|
595 Author's page: http://www.exelixis-lab.org/
|
|
|
596
|
|
|
597 Help: http://groups.google.com/group/raxml
|
|
|
598
|
|
|
599 Citing:
|
|
|
600 _______
|
|
|
601
|
|
|
602 Alexandros Stamatakis : “RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic
|
|
|
603 Analyses with Thousands of Taxa and Mixed Models”, Bioinformatics
|
|
|
604 22(21):2688–2690, 2006.
|
|
|
605 </help>
|
|
|
606 </tool>
|
