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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml-ng commit 73e57581d32cd1ffa9b234faa87fc2e2ac3ae37f
author iuc
date Sun, 21 Dec 2025 10:17:03 +0000
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-1:000000000000 0:21da84148596
1 <tool id="raxmlng" name="RAxML-NG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
2 <description>Maximum Likelihood based inference of large phylogenetic trees</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.2.2</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">RAxML-NG</xref>
9 </xrefs>
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">raxml-ng</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[
14 raxml-ng
15 $command
16 #if $command == '--consense':
17 $consensus_type
18 #end if
19 --msa '$infile'
20 --prefix galaxy
21 #if $model.model_type == 'single_gui':
22 #if $model.seq_type == 'multistate':
23 #set model_matrix = '""'.join(["MULTI", str($model.single_model.multi_state_count),"_",str($model.single_model.subst_matrix)])
24 #else:
25 #set model_matrix = str($model.single_model.subst_matrix)
26 #end if
27 #if str($model.rhas_model) in ['+G', '+R', '+I+G', '+I+R']:
28 #set model_rhas = '""'.join([str($model.rhas_model), str($model.rhas_cat_count)])
29 #else
30 #set model_rhas = str($model.rhas_model)
31 #end if
32 --model ${model_matrix}${model.base_freqs}${model_rhas}
33 #elif $model.model_type == 'single_string'
34 --model '${model.model_string}'
35 #elif $model.model_type == 'multi_file'
36 --model '$model.model_file'
37 --brlen $model.brlen_linkage
38 #end if
39 #set start_trees = []
40 #if $tree_file:
41 #set start_trees = start_trees + [str($tree_file)]
42 #end if
43 #if $tree_pars_count:
44 #set start_trees = start_trees + ['""'.join(["pars{", str($tree_pars_count), "}"])]
45 #end if
46 #if $tree_rand_count:
47 #set start_trees = start_trees + ['""'.join(["rand{", str($tree_rand_count), "}"])]
48 #end if
49 #set tree_str = '","'.join($start_trees)
50 #if $tree_str:
51 --tree $tree_str
52 #end if
53 #if $outgroup_name:
54 --outgroup '$outgroup_name'
55 #end if
56 #if $constraint_file:
57 --tree-constraint '$constraint_file'
58 #end if
59 #if $command == '--all' or $command == '--bootstrap':
60 #if $bs_metric
61 --bs-metric $bs_metric
62 #end if
63 #if $bs_mre:
64 --bs-trees autoMRE{$bs_reps}
65 --bs-cutoff $bs_cutoff
66 #else
67 --bs- trees $bs_reps
68 #end if
69 #elif $command == '--support':
70 #if $bs_metric
71 --bs-metric $bs_metric
72 #end if
73 --bs-trees $bs_trees
74 #elif $command == '--bsconverge':
75 --bs-cutoff $bs_cutoff
76 --bs-trees $bs_trees
77 #end if
78 #if $random_seed:
79 --seed $random_seed
80 #end if
81 #if $lh_epsilon:
82 --lh-epsilon $lh_epsilon
83 #end if
84 #if $lh_epsilon_triplet:
85 --lh-epsilon-triplet $lh_epsilon_triplet
86 #end if
87 #if $blmin:
88 --blmin $blmin
89 #end if
90 #if $blmax:
91 --blmax $blmax
92 #end if
93 $pat_comp
94 $site_repeats
95 $rate_scalers
96 #if $force:
97 --force $force
98 #end if
99 #if $log_level:
100 --log $log_level
101 #end if
102 #if $site_weights:
103 --site-weights $site_weights
104 #end if
105 --threads auto{\${GALAXY_SLOTS:-8}}
106 ]]></command>
107 <inputs>
108 <section name="general_opts" expanded="true" title="General options">
109 <param name="command" type="select" label="Analysis type">
110 <option value="--check">Check alignment correctness</option>
111 <!-- <option value="-parse">Convert alignment to a compressed binary format (RBA)</option> -->
112 <option value="--search" selected="true">Tree search (default)</option>
113 <option value="--search1">Tree search (FAST)</option>
114 <option value="--all">Tree search with branch support values (SLOW)</option>
115 <option value="--evaluate">Optimize branches and model parameters on a fixed topology</option>
116 <option value="--start">Generate parsimony and/or random starting trees</option>
117 <option value="--bootstrap">Bootstrap tree inference (SLOW)</option>
118 <option value="--support">Support value mapping from existing set of bootstrap trees</option>
119 <option value="--bsconverge">Bootstopping: Test bootstrap convergerge a posteriori</option>
120 <option value="--sitelh">Print per-site log-likelihoods</option>
121 <option value="--ancestral">Ancestral state reconstruction on a given tree</option>
122 <option value="--rfdist">RF: Compute pair-wise Robinson-Foulds distances between trees</option>
123 <option value="--consense">Build a consensus tree</option>
124 <option value="--terrace">Check whether a tree lies on a phylogenetic terrace</option>
125 </param>
126 <param name="infile" argument="--msa" type="data" format="fasta,phylip" label="Source file with aligned sequences"
127 help="At least four aligned genomes are needed for RAxML-NG." />
128 <conditional name="model">
129 <param name="model_type" type="select" display="radio" label="Model type">
130 <option value="single_gui" selected="true">Single model (GUI)</option>
131 <option value="single_string">Single model (string)</option>
132 <option value="multi_file">Partitioned model file</option>
133 </param>
134 <when value="single_gui">
135 <conditional name="single_model">
136 <param name="seq_type" type="select" display="radio" label="Sequence type">
137 <option value="nucleotide" selected="true">Nucleotide</option>
138 <option value="aminoacid">Amino Acid</option>
139 <option value="binary">Binary</option>
140 <option value="multistate">Multistate</option>
141 </param>
142 <when value="nucleotide">
143 <param name="subst_matrix" type="select" label="Matrix">
144 <option value="F81">F81</option>
145 <option value="GTR" selected="true">GTR</option>
146 <option value="HKY">HKY</option>
147 <option value="JC">JC</option>
148 <option value="K80">K80</option>
149 <option value="SYM">SYM</option>
150 <option value="TIM1">TIM1</option>
151 <option value="TIM2">TIM2</option>
152 <option value="TIM3">TIM3</option>
153 <option value="TN93">TN93</option>
154 <option value="TPM1">TPM1</option>
155 <option value="TPM2">TPM2</option>
156 <option value="TPM3">TPM3</option>
157 <option value="TVM">TVM</option>
158 </param>
159 </when>
160 <when value="aminoacid">
161 <param name="subst_matrix" type="select" label="Matrix">
162 <option value="BLOSUM62">BLOSUM62</option>
163 <option value="CPREV">CPREV</option>
164 <option value="DAYHOFF">DAYHOFF</option>
165 <option value="DCMUT">DCMUT</option>
166 <option value="FLU">FLU</option>
167 <option value="PROTGTR">GTR</option>
168 <option value="HIVB">HIVB</option>
169 <option value="HIVW">HIVW</option>
170 <option value="JTT">JTT</option>
171 <option value="JTT-DCMUT">JTT-DCMUT</option>
172 <option value="LG" selected="true">LG</option>
173 <option value="LG4M">LG4M</option>
174 <option value="LG4X">LG4X</option>
175 <option value="MTART">MTART</option>
176 <option value="MTMAM">MTMAM</option>
177 <option value="MTREV">MTREV</option>
178 <option value="MTZOA">MTZOA</option>
179 <option value="PMB">PMB</option>
180 <option value="RTREV">RTREV</option>
181 <option value="VT">VT</option>
182 <option value="WAG">WAG</option>
183 </param>
184 </when>
185 <when value="binary">
186 <param name="subst_matrix" type="select" label="Matrix">
187 <option value="BIN">BIN</option>
188 </param>
189 </when>
190 <when value="multistate">
191 <param name="multi_state_count" type="integer" value="2" label="Number of states" />
192 <param name="subst_matrix" type="select" label="Matrix">
193 <option value="MK">MULTIx_MK</option>
194 <option value="GTR">MULTIx_GTR</option>
195 </param>
196 </when>
197 </conditional>
198 <param name="base_freqs" type="select" label="Stationary base frequencies">
199 <option value="" selected="true">Default</option>
200 <option value="+FO">ML estimate</option>
201 <option value="+F">empirical</option>
202 <option value="+FE">equal</option>
203 </param>
204 <param name="rhas_model" type="select" label="Rate heterogeneity across sites (RHAS) model">
205 <option value="">None / default</option>
206 <option value="+G" selected="true">GAMMA</option>
207 <option value="+I">Inv</option>
208 <option value="+I+G">Inv+GAMMA</option>
209 <option value="+R">FreeRate</option>
210 <option value="+I+R">Inv+FreeRate</option>
211 </param>
212 <param name="rhas_cat_count" type="integer" value="" optional="true" label="Number of RHAS categories" help="Typical range: 2..10 (default: 4)"/>
213 </when>
214 <when value="single_string">
215 <param name="model_string" type="text" value="" optional="false" label="Model definition string" help="Help: https://github.com/amkozlov/raxml-ng/wiki/Input-data#single-model" >
216 <sanitizer>
217 <valid initial="string.ascii_letters,string.digits,string.punctuation">
218 <remove value="';"/>
219 </valid>
220 </sanitizer>
221 </param>
222 </when>
223 <when value="multi_file">
224 <param name="model_file" type="data" format="txt" label="Partitioned model file" help="Help: https://github.com/amkozlov/raxml-ng/wiki/Input-data#multiple-models" />
225 <param name="brlen_linkage" type="select" display="radio" label="Branch length linkage among partitions">
226 <option value="linked">Linked identical</option>
227 <option value="scaled" selected="true">Linked proportional</option>
228 <option value="unlinked">Unlinked</option>
229 </param>
230 </when>
231 </conditional>
232 </section>
233 <section name="tree_opts" expanded="false" title="Tree options">
234 <param name="tree_file" type="data" format="nhx" optional="true" label="User starting trees (NEWICK file)" />
235 <param name="tree_pars_count" type="integer" value="" optional="true" label="Number of PARSIMONY starting trees" />
236 <param name="tree_rand_count" type="integer" value="" optional="true" label="Number of RANDOM starting trees" />
237 <param name="outgroup_name" argument="--outgroup" type="text" value="" optional="true" label="Root a tree: Outgroup taxon name(s)" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed"/>
238 <param name="constraint_file" argument="--tree-constraint" type="data" format="txt" optional="true" label="Constraint tree" help="Topological constraint in NEWICK format (can be partial)"/>
239 <param name="consensus_type" type="select" display="radio" label="Consensus type">
240 <option value="strict">Strict</option>
241 <option value="mr" selected="true">Majority Rule (MR)</option>
242 <option value="mre">Majority Rule Extended (MRE)</option>
243 </param>
244 </section>
245 <section name="bootstrap_opts" expanded="false" title="Bootstrapping options">
246 <param name="bs_metric" type="select" multiple="true" display="checkboxes" label="Branch support metric">
247 <option value="fbp" selected="true">Felsenstein bootstrap</option>
248 <option value="tbe">Transfer bootstrap (TBE)</option>
249 </param>
250 <param name="bs_reps" type="integer" value="1000" min="1" max="10000" label="Number of replicates" />
251 <param name="bs_mre" type="boolean" checked="true" label="Use bootstopping (autoMRE convergence test)" />
252 <param name="bs_cutoff" type="float" value="0.03" min="0" max="1" label="Bootstopping cutoff" help="Cutoff threshold for the MRE-based convergence test" />
253 <param argument="--bs-trees" type="data" format="nhx" optional="true" label="Existing set of bootstrap trees"/>
254 </section>
255 <section name="safety_opts" expanded="false" title="Safety checks">
256 <param argument="--force" type="select" multiple="true" display="checkboxes" label="Disable safety checks (use with CAUTION!)">
257 <option value="perf">Performance-related (e.g. number of threads)</option>
258 <option value="msa">MSA-related (e.g. duplicate or gap-only sequences) </option>
259 <option value="model">Model-related (e,g, invalid state frequencies)</option>
260 </param>
261 </section>
262 <section name="advanced_opts" expanded="false" title="Advanced options">
263 <param name="random_seed" argument="--seed" type="integer" value="1" label="Random seed" />
264 <param argument="--lh-epsilon" type="float" value="" optional="true" label="Log-likelihood epsilon for tree search and model optimization" help="Default: 0.1"/>
265 <param argument="--lh-epsilon-triplet" type="float" value="" optional="true" label="Log-likelihood epsilon for branch length triplet optimization" help="Default: 1000"/>
266 <param argument="--blmin" type="float" value="" optional="true" label="MIN branch length" help="Default: 10^-6"/>
267 <param argument="--blmax" type="float" value="" optional="true" label="MAX branch length" help="Default: 100"/>
268 <param name="pat_comp" type="boolean" truevalue="--pat-comp off" falsevalue="" label="Disable alignment pattern compression" help="Default: NO" />
269 <param name="site_repeats" type="boolean" truevalue="--site-repeats off" falsevalue="" label="Disable site repeats optimization" help="Default: NO" />
270 <param name="rate_scalers" type="boolean" truevalue="--rate-scalers on" falsevalue="" label="ALWAYS use individual CLV scalers for each rate category" help="Default: use if MSA has >2000 taxa" />
271 <param name="log_level" argument="--log" type="select" optional="true" label="Log verbosity">
272 <option value="error">ERROR</option>
273 <option value="warning">WARNING</option>
274 <option value="result">RESULT</option>
275 <option value="info">INFO</option>
276 <option value="progress">PROGRESS</option>
277 <option value="verbose">VERBOSE</option>
278 <option value="debug">DEBUG</option>
279 </param>
280 <param argument="--site-weights" type="data" format="txt" optional="true" label="File with custom MSA column weights (positive integers only!)" />
281 </section>
282 </inputs>
283 <outputs>
284 <data format="txt" name="log" from_work_dir="galaxy.raxml.log" label="${tool.name} on ${on_string}: Log"/>
285 <!--
286 <data format="binary" name="rba" from_work_dir="galaxy.raxml.rba" label="${tool.name} on ${on_string}: RAxML Binary Alignment">
287 <filter>
288 general_opts['command'] in ["-parse", "-search", "-search1", "-all"]
289 </filter>
290 </data>
291 -->
292 <data format="nhx" name="bestTree" from_work_dir="galaxy.raxml.bestTree" label="${tool.name} on ${on_string}: Best-scoring ML Tree">
293 <filter>general_opts['command'] in ["--search", "--search1", "--all", "--evaluate"] </filter>
294 </data>
295 <data format="nhx" name="supportTree" from_work_dir="galaxy.raxml.support" label="${tool.name} on ${on_string}: ML Tree with branch support values">
296 <filter>general_opts['command'] in ["--all", "--support"] </filter>
297 </data>
298 <data format="nhx" name="bootstrapTrees" from_work_dir="galaxy.raxml.bootstraps" label="${tool.name} on ${on_string}: Bootstrap trees">
299 <filter>general_opts['command'] in ["--all", "--bootstrap"] </filter>
300 </data>
301 <data format="txt" name="bestModel" from_work_dir="galaxy.raxml.bestModel" label="${tool.name} on ${on_string}: Optimized model parameters">
302 <filter>general_opts['command'] in ["--search", "--search1", "--all", "--evaluate"]</filter>
303 </data>
304 <data format="nhx" name="startTree" from_work_dir="galaxy.raxml.startTree" label="${tool.name} on ${on_string}: Starting trees">
305 <filter>general_opts['command'] in ["--search", "--search1", "--all", "--start"] </filter>
306 </data>
307 <data format="txt" name="siteLH" from_work_dir="galaxy.raxml.siteLH" label="${tool.name} on ${on_string}: Per-site log-likelihoods">
308 <filter>general_opts['command'] == "--sitelh"</filter>
309 </data>
310 <data format="txt" name="rfDistances" from_work_dir="galaxy.raxml.rfDistances" label="${tool.name} on ${on_string}: Pair-wise RF distances">
311 <filter>general_opts['command'] == "--rfdist"</filter>
312 </data>
313 <data format="txt" name="terrace" from_work_dir="galaxy.raxml.terrace" label="${tool.name} on ${on_string}: Terrace">
314 <filter>general_opts['command'] == "--terrace"</filter>
315 </data>
316 <data format="nhx" name="consensusTreeSTRICT" from_work_dir="galaxy.raxml.consensusTreeSTRICT" label="${tool.name} on ${on_string}: Consensus Tree (strict)">
317 <filter>general_opts['command'] == "--consense" and tree_opts['consensus_type'] == "strict" </filter>
318 </data>
319 <data format="nhx" name="consensusTreeMR" from_work_dir="galaxy.raxml.consensusTreeMR" label="${tool.name} on ${on_string}: Consensus Tree (MR)">
320 <filter>general_opts['command'] == "--consense" and tree_opts['consensus_type'] == "mr" </filter>
321 </data>
322 <data format="nhx" name="consensusTreeMRE" from_work_dir="galaxy.raxml.consensusTreeMRE" label="${tool.name} on ${on_string}: Consensus Tree (MRE)">
323 <filter>general_opts['command'] == "--consense" and tree_opts['consensus_type'] == "mre" </filter>
324 </data>
325 <data format="nhx" name="ancestralTree" from_work_dir="galaxy.raxml.ancestralTree" label="${tool.name} on ${on_string}: Ancestral None-labeled Tree">
326 <filter>general_opts['command'] == "--ancestral" </filter>
327 </data>
328 <data format="txt" name="ancestralStates" from_work_dir="galaxy.raxml.ancestralStates" label="${tool.name} on ${on_string}: Ancestral Sequences">
329 <filter>general_opts['command'] == "--ancestral" </filter>
330 </data>
331 <data format="txt" name="ancestralProbs" from_work_dir="galaxy.raxml.ancestralProbs" label="${tool.name} on ${on_string}: Ancestral Marginal Probabilities">
332 <filter>general_opts['command'] == "--ancestral" </filter>
333 </data>
334 </outputs>
335 <tests>
336 <test expect_num_outputs="4">
337 <section name="general_opts">
338 <param name="command" value="--search"/>
339 <param name="infile" value="dna.phy"/>
340 <conditional name="model">
341 <param name="model_type" value="single_gui"/>
342 <conditional name="single_model">
343 <param name="seq_type" value="nucleotide"/>
344 <param name="subst_matrix" value="HKY"/>
345 </conditional>
346 </conditional>
347 </section>
348 <section name="tree_opts">
349 <param name="tree_pars_count" value="6"/>
350 <param name="tree_rand_count" value="4"/>
351 </section>
352 <section name="advanced_opts">
353 <param name="random_seed" value="1"/>
354 </section>
355 <output name="log">
356 <assert_contents>
357 <has_text text="Final LogLikelihood:"/>
358 <has_text text="Elapsed time:"/>
359 </assert_contents>
360 </output>
361 <output name="startTree" file="tree10.raxml.galaxy" ftype="nhx"/>
362 <output name="bestModel">
363 <assert_contents>
364 <has_n_columns n="2" sep="="/>
365 <has_n_lines n="1"/>
366 <has_text text="HKY"/>
367 </assert_contents>
368 </output>
369 <output name="bestTree" ftype="nhx">
370 <assert_contents>
371 <has_text_matching expression="Frog"/>
372 </assert_contents>
373 </output>
374 </test>
375 <test expect_num_outputs="2">
376 <section name="general_opts">
377 <param name="command" value="--consense"/>
378 <param name="infile" value="dna.phy"/>
379 </section>
380 <section name="tree_opts">
381 <param name="tree_file" value="tree10.raxml.galaxy"/>
382 <param name="consensus_type" value="mr"/>
383 </section>
384 <section name="advanced_opts">
385 <param name="random_seed" value="1"/>
386 </section>
387 <output name="log">
388 <assert_contents>
389 <has_text text="run mode: Build consensus tree"/>
390 <has_text text="Elapsed time:"/>
391 </assert_contents>
392 </output>
393 <output name="consensusTreeMR" ftype="nhx">
394 <assert_contents>
395 <has_text text="Cow"/>
396 <has_text text="Frog"/>
397 <has_n_lines n="1"/>
398 </assert_contents>
399 </output>
400 </test>
401 </tests>
402 <help><![CDATA[
403 RAxML-NG is a phylogenetic tree inference tool which uses Maximum-Likelihood (ML) optimality criterion.
404 Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves,
405 which allows to quickly navigate to the best-known ML tree.
406 RAxML-NG is a successor of RAxML 8.x (Stamatakis 2014).
407
408 Documentation: https://github.com/amkozlov/raxml-ng/wiki
409
410 .. _RAxML-NG: http://www.exelixis-lab.org/web/software/raxml-ng/
411
412 ]]></help>
413 <citations>
414 <citation type="doi">10.1093/bioinformatics/btz305</citation>
415 </citations>
416 </tool>