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planemo upload commit 2c71c5e5604b9c05648b883fddbb163a8e03c807
author tiagoantao
date Tue, 03 Nov 2015 16:27:41 -0500
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1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
3 <requirements>
4 <requirement type='package' version="8.2.4">raxml</requirement>
5 </requirements>
6 <command interpreter="python">raxml.py
7 ## Required parameters
8 ## Program name and threads are hard-coded as they are dependent on the binary and threads are specified in the Galaxy's tool configuration
9 ## binary is hard-coded to the pthreads enabled raxml executable
10 --binary "raxmlHPC-PTHREADS"
11 ## (-T)
12 --threads \${GALAXY_SLOTS:-1}
13 ## (-s)
14 --source $infile
15 ## (-m)
16 --model_type $search_model_selector.model_type
17 --base_model $search_model_selector.base_model
18 #if str( $search_model_selector.model_type ) == 'aminoacid':
19 $search_model_selector.aa_model_empirical_base_frequencies
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 $selExtraOpts.search_complete_random_tree
59 ## (-D)
60 $selExtraOpts.ml_search_convergence
61 ## (-e)
62 #if $selExtraOpts.model_opt_precision:
63 --model_opt_precision $selExtraOpts.model_opt_precision
64 #end if
65 ## (-E)
66 #if $selExtraOpts.excludefile:
67 --excludefile $selExtraOpts.excludefile
68 #end if
69 ## (-f)
70 #if $selExtraOpts.search_algorithm:
71 --search_algorithm $selExtraOpts.search_algorithm
72 #end if
73 ## (-F)
74 $selExtraOpts.save_memory_cat_model
75 ## (-g)
76 #if $selExtraOpts.groupingfile:
77 --groupingfile $selExtraOpts.groupingfile
78 #end if
79 ## (-G)
80 #if $selExtraOpts.enable_evol_heuristics:
81 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics
82 #end if
83 ## (-i)
84 #if $selExtraOpts.initial_rearrangement_setting:
85 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting
86 #end if
87 ## (-I)
88 #if $selExtraOpts.posterior_bootstopping_analysis:
89 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis
90 #end if
91 ## (-J)
92 #if $selExtraOpts.majority_rule_consensus:
93 --majority_rule_consensus $selExtraOpts.majority_rule_consensus
94 #end if
95 ## (-k)
96 $selExtraOpts.print_branch_lengths
97 ## (-K)
98 #if str ($selExtraOpts.multistate_sub_model) != "":
99 --multistate_sub_model $selExtraOpts.multistate_sub_model
100 #end if
101 ## (-m) - see elsewhere
102 ## (-M)
103 $selExtraOpts.estimate_individual_branch_lengths
104 ## (-n) - see elsewhere
105 ## (-o)
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 $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 #end if
157
158 </command>
159 <inputs>
160 ## (-s)
161 <param type="data" format="fasta,phylip" name="infile" label="Source file"/>
162 ## (-m)
163 <conditional name="search_model_selector">
164 <param name="model_type" type="select" label="Model Type">
165 <option value="nucleotide" selected="true">Nucleotide</option>
166 <option value="aminoacid">Amino Acid</option>
167 <option value="binary">Binary</option>
168 <option value="multistate">Multistate</option>
169 </param>
170 <when value="nucleotide">
171 ## Nucleotide substitution models
172 <param name="base_model" type="select" label="Substitution Model">
173 <option value="GTRCAT">GTRCAT</option>
174 <option value="GTRCATI">GTRCATI</option>
175 <option value="GTRGAMMA" select="true">GTRGAMMA</option>
176 <option value="GTRGAMMAI">GTRGAMMAI</option>
177 </param>
178 </when>
179 ## Aminoacid substitution models
180 <when value="aminoacid">
181 <param name="aa_model_empirical_base_frequencies"
182 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" />
183 <param name="base_model" type="select" label="Substitution Model (-m)">
184 <option value="PROTCAT" select="true">PROTCAT</option>
185 <option value="PROTCATI">PROTCATI</option>
186 <option value="PROTGAMMA">PROTGAMMA</option>
187 <option value="PROTGAMMAI">PROTGAMMAI</option>
188 </param>
189 <param name="aa_search_matrix" type="select" label="Matrix">
190 <option value="DAYHOFF" select="true">DAYHOFF</option>
191 <option value="DCMUT">DCMUT</option>
192 <option value="JTT">JTT</option>
193 <option value="MTREV">MTREV</option>
194 <option value="WAG">WAG</option>
195 <option value="RTREV">RTREV</option>
196 <option value="CPREV">CPREV</option>
197 <option value="VT">VT</option>
198 <option value="BLOSUM62">BLOSUM62</option>
199 <option value="MTMAM">MTMAM</option>
200 <option value="LG">LG</option>
201 <option value="MTART">MTART</option>
202 <option value="MTZOA">MTZOA</option>
203 <option value="PMB">PMB</option>
204 <option value="HIVB">HIVB</option>
205 <option value="HIVW">HIVW</option>
206 <option value="JTTDCMUT">JTTDCMUT</option>
207 <option value="FLU">FLU</option>
208 <option value="DUMMY">DUMMY</option>
209 <option value="DUMMY2">DUMMY2</option>
210 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
211 <option value="GTR">GTR</option>
212 </param>
213 </when>
214 ## Binary substitution models
215 <when value="binary">
216 <param name="base_model" type="select" label="Substitution Model">
217 <option value="BINCAT">BINCAT</option>
218 <option value="BINCATI">BINCATI</option>
219 <option value="BINGAMMA">BINGAMMA</option>
220 <option value="BINGAMMAI">BINGAMMAI</option>
221 </param>
222 </when>
223 ## Multi-state substitution models
224 <when value="multistate">
225 <param name="base_model" type="select" label="Substitution Model">
226 <option value="MULTICAT">MULTICAT</option>
227 <option value="MULTICATI">MULTICATI</option>
228 <option value="MULTIGAMMA">MULTIGAMMA</option>
229 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
230 </param>
231 </when>
232 </conditional>
233 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random
234 seed used for the parsimony inferences" />
235 <conditional name="selExtraOpts">
236 <param name="extraOptions" type="select" label="RAxML options to use"
237 help="The required minimal settings are the input file and the
238 substitution model. To specify extra options select the 'Full option list'">
239 <option value="required">Required options only</option>
240 <option value="full">Full option list</option>
241 </param>
242 <when value="full">
243 ## (-N/#)
244 <param name="number_of_runs" type="integer" size="8" value=""
245 label="Number of runs" help="Specify the number of
246 alternative runs (-N|#) on distinct starting trees In combination
247 with the '-b' option will invoke a multiple boostrap analysis.
248 You can add the bootstopping criteria by choosing the autoMR,
249 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
250 providing a number here. Bootstopping will only work in
251 combination with '-x' or '-b'."
252 optional="True" />
253 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True">
254 <option value="" selected="yes"></option>
255 <option value="autoMR">autoMR</option>
256 <option value="autoMRE">autoMRE</option>
257 <option value="autoMRE_IGN">autoMRE_IGN</option>
258 <option value="autoFC">autoFC</option>
259 </param>
260 ## Alphabetical Listing of Advanced Options
261 ## (-a)
262 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" />
263 ## (-A)
264 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True">
265 <option value="" selected="yes"></option>
266 <option value="S6A">S6A</option>
267 <option value="S6B">S6B</option>
268 <option value="S6C">S6C</option>
269 <option value="S6D">S6D</option>
270 <option value="S6E">S6E</option>
271 <option value="S7A">S7A</option>
272 <option value="S7B">S7B</option>
273 <option value="S7C">S7C</option>
274 <option value="S7D">S7D</option>
275 <option value="S7E">S7E</option>
276 <option value="S7F">S7F</option>
277 <option value="S16">S16</option>
278 <option value="S16A">S16A</option>
279 <option value="S16B">S16B</option>
280 </param>
281 ## (-b)
282 <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true' optional="True" />
283 ## (-x)
284 <param name="rapid_bootstrap_random_seed" type="integer" value='' size="7" label="Rapid bootstrapping random seed" 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." />
285 ## (-B)
286 <param name="cutoff_threshold" type="float" size="8" label="MR Cutoff threshold" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" />
287 ## (-c)
288 <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" />
289 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now.
290 ## (-d)
291 <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="--search_complete_random_tree" falsevalue="" display="checkboxes" label="Start ML optimization from a complete random starting tree" />
292 ## (-D)
293 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" />
294 ## (-e)
295 <param name="model_opt_precision" type="float" size="8" label="Model optimization precision" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" />
296 ## (-E)
297 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" />
298 ## (-f)
299 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True">
300 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
301 <option value="A">Compute marginal ancestral states (A)</option>
302 <option value="b">Draw bipartition information (b)</option>
303 <option value="c">Check if the alignment can be read (c)</option>
304 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option>
305 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
306 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
307 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
308 <option value="j">Generate bootstrapped alignment files (j)</option>
309 <option value="J">Compute SH-like support values for the -t tree (J)</option>
310 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
311 <option value="n">Compute log likelihood score for -z trees (n)</option>
312 <option value="o">Use old slower search algorithm (o)</option>
313 <option value="p">Stepwise MP addition of new sequences (p)</option>
314 <option value="q">Fast quartet calculator (q)</option>
315 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
316 <option value="s">Split a multi-gene alignment (s)</option>
317 <option value="S">Compute site-specific placement bias (S)</option>
318 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
319 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
320 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
321 <option value="v">Classify environmental sequences (v)</option>
322 <option value="w">Compute ELW-test on -z trees (w)</option>
323 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
324 <option value="y">Classify environmental sequences into a reference tree (y)</option>
325 </param>
326 ## (-F)
327 <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="--save_memory_cat_model" falsevalue="" display="checkboxes" label="ML tree searches under CAT model" 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" />
328 ## (-g)
329 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" />
330 ## (-G)
331 <param name="enable_evol_heuristics" type="float" size="8" label="Enable the ML-based evolutionary placement algorithm heuristics" 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" >
332 <validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/>
333 </param>
334 ## (-i)
335 <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting" optional="True" />
336 ## (-I)
337 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True">
338 <option value="" selected="True"></option>
339 <option value="autoFC">Frequency-based criterion (autoFC)</option>
340 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
341 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
342 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
343 </param>
344 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy
345 ## (-J)
346 <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True">
347 <option value="" selected="True"></option>
348 <option value="MR">Majority-rule consensus tree (MR)</option>
349 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
350 <option value="STRICT">Strict consensus tree (STRICT)</option>
351 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
352 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
353 </param>
354 ## (-k)
355 <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." optional="True" />
356 ## (-K)
357 <param name="multistate_sub_model" type="select" label="Specify a
358 multi-state substitution model" optional="True">
359 <option value="" selected="true"></option>
360 <option value="GTR">GTR</option>
361 <option value="ORDERED">ORDERED</option>
362 <option value="MK">MK</option>
363 </param>
364 ## (-M)
365 <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes" label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-q)." optional="True" />
366 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files
367 ## (-o)
368 <param name="outgroup_name" type="text" size="40" value="" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" />
369 ## (-O)
370 <param name="disable_undetermined_seq_check" type="boolean" checked="no" 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." />
371 <param name="external_protein_model" format="txt" type="data" label="External AA substitution model" 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" />
372 ## (-q)
373 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" 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." />
374 ## (-r)
375 <param name="constraint_file" format="txt" type="data" label="Binary constraint tree" 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." />
376 ## (-R)
377 <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" 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." />
378 ## (-s) source file option is in the required options section
379 ## (-S)
380 <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" 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 '()&lt;&gt;[]{}' to define stem regions and pseudoknots."/>
381 ## (-t)
382 <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True" help="Specify a user starting tree file name in Newick format." />
383 ## (-T) is hard-coded in the required options section
384 <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" />
385 ## (-U)
386 <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" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" />
387 ## (-V)
388 <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." optional="True" />
389 ## (-W)
390 <param name="sliding_window_size" type="integer" size="5" value="" label="Sliding window size" 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'" />
391 ## (-x) - see it by the (-b)
392 ## (-y)
393 <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes" label="Compute a randomized parsimony starting tree only" 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." />
394 ## (-z)
395 <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file" 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" />
396 </when> ## full option list
397 </conditional> ## END $selExtraOpts
398 </inputs>
399 <outputs>
400 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
401 ## REQUIRED
402 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
403 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
404 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
405 </data>
406 <data format="txt" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
407 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
408 </data>
409 <data format="txt" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
410 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
411 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
412 </data>
413 <data format="txt" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
414 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
415 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
416 </data>
417 ## ADVANCED
418 <data format="txt" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
419 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
420 <filter>selExtraOpts['extraOptions'] == "full"</filter>
421 </data>
422 <data format="txt" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
423 <filter>(selExtraOpts['extraOptions'] == 'full')</filter>
424 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '' or selExtraOpts['bootseed'] == '') and (selExtraOpts['search_algorithm'] == 'a')</filter>
425 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
426 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter>
427 </data>
428 <data format="txt" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
429 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
430 <filter>(selExtraOpts['multiple_model'] != '')</filter>
431 </data>
432 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
433 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
434 <filter>selExtraOpts['multiple_model'] is not None </filter>
435 </data>
436 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
437 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
438 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
439 <filter>(selExtraOpts['bootseed'] == '')</filter>
440 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
441 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
442 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
443 </data>
444 <data format="txt" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
445 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
446 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
447 <filter>selExtraOpts['bootseed'] == ''</filter>
448 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
449 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
450 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
451 </data>
452 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
453 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
454 <filter>(selExtraOpts['multiple_model'] is not None)</filter>
455 </data>
456 <data format="txt" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
457 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
458 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
459 <filter>(selExtraOpts['bootseed'] == '')</filter>
460 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
461 <filter>(selExtraOpts['constraint_file'] is None)</filter>
462 <filter>(selExtraOpts['groupingfile'] is None)</filter>
463 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter>
464 <filter>(selExtraOpts['start_tree_file'] is None)</filter>
465 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
466 </data>
467 <data format="txt" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
468 <filter>selExtraOpts['extraOptions'] == "full"</filter>
469 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
470 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
471 </data>
472 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
473 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
474 <filter>selExtraOpts['extraOptions'] == "full"</filter>
475 </data>
476 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
477 <filter>selExtraOpts['extraOptions'] == "full"</filter>
478 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
479 </data>
480 <data format="txt" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
481 <filter>selExtraOpts['extraOptions'] == "full"</filter>
482 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter>
483 </data>
484 <data format="txt" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
485 <filter>selExtraOpts['extraOptions'] == "full"</filter>
486 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter>
487 </data>
488 <data format="txt" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
489 <filter>selExtraOpts['extraOptions'] == "full"</filter>
490 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter>
491 </data>
492 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
493 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
494 <filter>selExtraOpts['extraOptions'] == "full"</filter>
495 </data>
496 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
497 <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
498 <filter>selExtraOpts['extraOptions'] == "full"</filter>
499 </data>
500 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
501 <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
502 <filter>selExtraOpts['extraOptions'] == "full"</filter>
503 </data>
504 </outputs>
505 <tests>
506 <test>
507 <param name="extraOptions" value="required"/>
508 <param name="infile" value="dna.phy"/>
509 <param name="model_type" value="nucleotide"/>
510 <param name="base_model" value="GTRCAT"/>
511 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy">
512 <output name="bestTreeReq"/>
513 <assert_contents>
514 <has_text_matching expression="Frog" />
515 </assert_contents>
516 </output>
517 </test>
518 </tests>
519 <help>
520 Title:
521 ______
522 Randomized Axelerated Maximum Likelihood
523
524 Author:
525 _______
526 Alexandros Stamatakis
527
528 Description:
529 ____________
530
531 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic
532 trees. The program is explicitly being developed to efficiently infer trees for
533 extremely large datasets, either in terms of the number of taxa and/or the
534 sequence length.
535
536 This wrapper works with the RAxML version 8.2.4.
537
538 URL:
539 ____
540 Author's page: http://www.exelixis-lab.org/
541
542 Help: http://groups.google.com/group/raxml
543
544
545 Tool development:
546 -----------------
547 Oleksandr Moskalenko with adaptations from Tiago Antao.
548
549 </help>
550 <citations>
551 <citation type="doi">10.1093/bioinformatics/btu033</citation>
552 <citation type="bibtex">
553 @article{stamatakis2014raxml,
554 title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
555 author={Stamatakis, Alexandros},
556 journal={Bioinformatics},
557 volume={30},
558 number={9},
559 pages={1312--1313},
560 year={2014},
561 publisher={Oxford Univ Press}}
562 </citation>
563 </citations>
564 </tool>