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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
author iuc
date Mon, 14 Nov 2016 14:03:39 -0500
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children ba29b5e2a4be
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1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.2">
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 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
9 ## (-T)
10 ## Cannot have --threads 1
11 #set $slots = $getVar('GALAXY_SLOTS', 1)
12 #if $slots == 1:
13 --binary "raxmlHPC"
14 --threads 1
15 #else:
16 --binary "raxmlHPC-PTHREADS"
17 --threads $slots
18 #end if
19 ## (-s)
20 --source "$infile"
21 ## (-m)
22 --model_type $search_model_selector.model_type
23 --base_model $search_model_selector.base_model
24 #if str( $search_model_selector.model_type ) == 'aminoacid':
25 $search_model_selector.aa_model_empirical_base_frequencies
26 #if $search_model_selector.aa_search_matrix:
27 --aa_search_matrix $search_model_selector.aa_search_matrix
28 #end if
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 $selExtraOpts.secondary_structure_model
48 #end if
49 ## (-b)
50 #if str($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 $selExtraOpts.sliding_window_size
145 #end if
146 ## (-x)
147 #if str($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>
169 <param type="data" format="fasta,phylip" name="infile" label="Source file" help="(-s)"/>
170 <conditional name="search_model_selector">
171 <param name="model_type" type="select" label="Model Type" help="(--model_type)">
172 <option value="nucleotide" selected="true">Nucleotide</option>
173 <option value="aminoacid">Amino Acid</option>
174 <option value="binary">Binary</option>
175 <option value="multistate">Multistate</option>
176 </param>
177 <when value="nucleotide">
178 <param name="base_model" type="select" label="Substitution Model" help="--base-model">
179 <option value="GTRCAT">GTRCAT</option>
180 <option value="GTRCATI">GTRCATI</option>
181 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
182 <option value="GTRGAMMAI">GTRGAMMAI</option>
183 </param>
184 </when>
185 <when value="aminoacid">
186 <param name="aa_model_empirical_base_frequencies"
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>
190 <option value="PROTCATI">PROTCATI</option>
191 <option value="PROTGAMMA">PROTGAMMA</option>
192 <option value="PROTGAMMAI">PROTGAMMAI</option>
193 </param>
194 <param name="aa_search_matrix" type="select" label="Matrix" help="(--aa_search_matrix)">
195 <option value="DAYHOFF" selected="true">DAYHOFF</option>
196 <option value="DCMUT">DCMUT</option>
197 <option value="JTT">JTT</option>
198 <option value="MTREV">MTREV</option>
199 <option value="WAG">WAG</option>
200 <option value="RTREV">RTREV</option>
201 <option value="CPREV">CPREV</option>
202 <option value="VT">VT</option>
203 <option value="BLOSUM62">BLOSUM62</option>
204 <option value="MTMAM">MTMAM</option>
205 <option value="LG">LG</option>
206 <option value="MTART">MTART</option>
207 <option value="MTZOA">MTZOA</option>
208 <option value="PMB">PMB</option>
209 <option value="HIVB">HIVB</option>
210 <option value="HIVW">HIVW</option>
211 <option value="JTTDCMUT">JTTDCMUT</option>
212 <option value="FLU">FLU</option>
213 <option value="DUMMY">DUMMY</option>
214 <option value="DUMMY2">DUMMY2</option>
215 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
216 <option value="GTR">GTR</option>
217 </param>
218 </when>
219 <when value="binary">
220 <param name="base_model" type="select" label="Substitution Model" help="(--base_model)">
221 <option value="BINCAT">BINCAT</option>
222 <option value="BINCATI">BINCATI</option>
223 <option value="BINGAMMA">BINGAMMA</option>
224 <option value="BINGAMMAI">BINGAMMAI</option>
225 </param>
226 </when>
227 <when value="multistate">
228 <param name="base_model" type="select" label="Substitution Model">
229 <option value="MULTICAT">MULTICAT</option>
230 <option value="MULTICATI">MULTICATI</option>
231 <option value="MULTIGAMMA">MULTIGAMMA</option>
232 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
233 </param>
234 </when>
235 </conditional>
236 <conditional name="selExtraOpts">
237 <param name="extraOptions" type="select" label="RAxML options to use"
238 help="The required minimal settings are the input file and the
239 substitution model. To specify extra options select the 'Full option list'">
240 <option value="required">Required options only</option>
241 <option value="full">Full option list</option>
242 </param>
243 <when value="required" />
244 <when value="full">
245 <param name="number_of_runs" type="integer" value=""
246 label="Number of runs" help="Specify the number of
247 alternative runs (-N|#) on distinct starting trees In combination
248 with the '-b' option will invoke a multiple boostrap analysis.
249 You can add the bootstopping criteria by choosing the autoMR,
250 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
251 providing a number here. Bootstopping will only work in
252 combination with '-x' or '-b'."
253 optional="True" />
254 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True" help="--number_of_runs_bootstop">
255 <option value="" selected="yes"></option>
256 <option value="autoMR">autoMR</option>
257 <option value="autoMRE">autoMRE</option>
258 <option value="autoMRE_IGN">autoMRE_IGN</option>
259 <option value="autoFC">autoFC</option>
260 </param>
261 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" help="(-a)" />
262 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True"
263 help="(--secondary_structure_model)">
264 <option value="" selected="yes"></option>
265 <option value="S6A">S6A</option>
266 <option value="S6B">S6B</option>
267 <option value="S6C">S6C</option>
268 <option value="S6D">S6D</option>
269 <option value="S6E">S6E</option>
270 <option value="S7A">S7A</option>
271 <option value="S7B">S7B</option>
272 <option value="S7C">S7C</option>
273 <option value="S7D">S7D</option>
274 <option value="S7E">S7E</option>
275 <option value="S7F">S7F</option>
276 <option value="S16">S16</option>
277 <option value="S16A">S16A</option>
278 <option value="S16B">S16B</option>
279 </param>
280 <param name="bootseed" type="integer" value="" label="Random number for non-parametric bootstrapping" optional="True" help="(--bootseed)"/>
281 <param name="rapid_bootstrap_random_seed" type="integer" value='' label="Rapid bootstrapping random seed" optional="True"
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)" />
283 <param name="cutoff_threshold" type="float" label="MR Cutoff threshold" value=""
284 help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1. (-B)" optional="True"/>
285 <param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" help="(-c)" />
286 <!-- (-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=""
288 display="checkboxes" label="Start ML optimization from a complete random starting tree" help="(--search_complete_random_tree)"/>
289 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue=""
290 label="ML search convergence criterion" help="(--ml_search_convergence)" />
291 <param name="model_opt_precision" type="float" label="Model optimization precision" value=""
292 help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used (--model_opt_precision)" optional="True" />
293 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" help="(-E)" />
294 <param name="search_algorithm" type="select" label="Algorithm to execute" help="(-f)" optional="True">
295 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
296 <option value="A">Compute marginal ancestral states (A)</option>
297 <option value="b">Draw bipartition information (b)</option>
298 <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>
300 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
301 <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>
303 <option value="j">Generate bootstrapped alignment files (j)</option>
304 <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>
306 <option value="n">Compute log likelihood score for -z trees (n)</option>
307 <option value="o">Use old slower search algorithm (o)</option>
308 <option value="p">Stepwise MP addition of new sequences (p)</option>
309 <option value="q">Fast quartet calculator (q)</option>
310 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
311 <option value="s">Split a multi-gene alignment (s)</option>
312 <option value="S">Compute site-specific placement bias (S)</option>
313 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
314 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
315 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
316 <option value="v">Classify environmental sequences (v)</option>
317 <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>
319 <option value="y">Classify environmental sequences into a reference tree (y)</option>
320 </param>
321 <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="--save_memory_cat_model" falsevalue=""
322 display="checkboxes" label="ML tree searches under CAT model" optional="True"
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)" />
324 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" help="(-g)" />
325 <param name="enable_evol_heuristics" type="float" label="Enable the ML-based evolutionary placement algorithm heuristics"
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" >
327 <validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/>
328 </param>
329 <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" help="(-i)"/>
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>
333 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
334 <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>
336 </param>
337 <!-- (-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)">
339 <option value="" selected="True"></option>
340 <option value="MR">Majority-rule consensus tree (MR)</option>
341 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
342 <option value="STRICT">Strict consensus tree (STRICT)</option>
343 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
344 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
345 </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" />
347 <param name="multistate_sub_model" type="select" optional="True" label="Specify a multi-state substitution model" help="(-K)">
348 <option value="" selected="true"></option>
349 <option value="GTR">GTR</option>
350 <option value="ORDERED">ORDERED</option>
351 <option value="MK">MK</option>
352 </param>
353 <param name="estimate_individual_branch_lengths" type="boolean" checked="no"
354 truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes"
355 label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-M)." optional="True" />
356 <param name="outgroup_name" type="text" value="" label="Outgroup name"
357 help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed. (-o)" optional="True" />
358 <param name="disable_undetermined_seq_check" type="boolean" checked="no"
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." />
360 <param name="external_protein_model" format="txt" type="data" label="External AA 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" />
362 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" 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)" />
364 <param name="constraint_file" format="txt" type="data" label="Binary constraint tree" optional="True"
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)" />
366 <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" optional="True"
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)" />
368 <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" optional="True"
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)"/>
370 <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True"
371 help="Specify a user starting tree file name in Newick format. (-t)" />
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"
373 help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity. (-T)" optional="True" />
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"
375 help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments. (-U)" optional="True" />
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" />
377 <param name="sliding_window_size" type="integer" value="" label="Sliding window size" optional="True"
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)" />
379 <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes"
380 label="Compute a randomized parsimony starting tree only" optional="True"
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." />
382 <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file"
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" />
384 <param name="random_seed" type="integer" value="1234567890" label="Random
385 seed used for the parsimony inferences" help="(--random_seed)"/>
386 </when>
387 </conditional>
388 </inputs>
389 <outputs>
390 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
391 <!-- REQUIRED -->
392 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
393 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
394 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
395 </data>
396 <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
397 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
398 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
399 </data>
400 <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
401 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
402 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
403 </data>
404 <!-- ADVANCED -->
405 <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
406 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
407 <filter>selExtraOpts['extraOptions'] == "full"</filter>
408 </data>
409 <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
410 <!-- <filter>(selExtraOpts['extraOptions'] == 'full')</filter> -->
411 <!-- <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
412 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter> -->
413 </data>
414 <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
415 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
416 <filter>(selExtraOpts['multiple_model'] != '')</filter>
417 </data>
418 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
419 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
420 <filter>selExtraOpts['multiple_model'] is not None </filter>
421 </data>
422 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
423 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
424 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
425 <filter>(selExtraOpts['bootseed'] == '')</filter>
426 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
427 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
428 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
429 </data>
430 <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
431 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
432 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
433 <filter>selExtraOpts['bootseed'] == ''</filter>
434 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
435 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
436 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
437 </data>
438 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
439 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
440 <filter>(selExtraOpts['multiple_model'] is not None)</filter>
441 </data>
442 <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
443 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
444 <!--
445 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
446 <filter>(selExtraOpts['bootseed'] == '')</filter>
447 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
448 <filter>(selExtraOpts['constraint_file'] is None)</filter>
449 <filter>(selExtraOpts['groupingfile'] is None)</filter>
450 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter>
451 <filter>(selExtraOpts['start_tree_file'] is None)</filter>
452 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
453 -->
454 </data>
455 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
456 <filter>selExtraOpts['extraOptions'] == "full"</filter>
457 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
458 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
459 </data>
460 <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>
462 <filter>selExtraOpts['extraOptions'] == "full"</filter>
463 </data>
464 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
465 <filter>selExtraOpts['extraOptions'] == "full"</filter>
466 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
467 </data>
468 <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
469 <filter>selExtraOpts['extraOptions'] == "full"</filter>
470 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter>
471 </data>
472 <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
473 <filter>selExtraOpts['extraOptions'] == "full"</filter>
474 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter>
475 </data>
476 <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
477 <filter>selExtraOpts['extraOptions'] == "full"</filter>
478 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter>
479 </data>
480 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
481 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
482 <filter>selExtraOpts['extraOptions'] == "full"</filter>
483 </data>
484 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
485 <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
486 <filter>selExtraOpts['extraOptions'] == "full"</filter>
487 </data>
488 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
489 <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
490 <filter>selExtraOpts['extraOptions'] == "full"</filter>
491 </data>
492 </outputs>
493 <tests>
494 <test>
495 <param name="extraOptions" value="required"/>
496 <param name="infile" value="dna.phy"/>
497 <param name="model_type" value="nucleotide"/>
498 <param name="base_model" value="GTRCAT"/>
499 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" />
500 <output name="bestTree">
501 <assert_contents>
502 <has_text_matching expression="Frog" />
503 </assert_contents>
504 </output>
505 </test>
506 <test>
507 <param name="extraOptions" value="full"/>
508 <param name="infile" value="dna.fasta"/>
509 <param name="model_type" value="nucleotide"/>
510 <param name="base_model" value="GTRCAT"/>
511 <param name="number_of_runs" value="5"/>
512 <output name="parsimonyTree">
513 <assert_contents>
514 <has_text_matching expression="Chicken" />
515 <has_text_matching expression="RUN.4" />
516 </assert_contents>
517 </output>
518 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" lines_diff="30"/>
519 <output name="bestTree">
520 <assert_contents>
521 <has_text_matching expression="Whale" />
522 </assert_contents>
523 </output>
524 </test>
525 </tests>
526 <help>
527
528 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
530 extremely large datasets, either in terms of the number of taxa and/or the
531 sequence length.
532
533
534 .. _RAxML: http://www.exelixis-lab.org/
535
536
537 **Tool development**:
538
539 Oleksandr Moskalenko with adaptations from Tiago Antao.
540
541 </help>
542 <citations>
543 <citation type="doi">10.1093/bioinformatics/btu033</citation>
544 </citations>
545 </tool>