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comparison raxml.xml @ 20:d930ea30718d draft

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planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501
author tiagoantao
date Tue, 03 Nov 2015 15:44:56 -0500
parents 2c55b607264c
children 48526baa210f
comparison
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19:2c55b607264c 20:d930ea30718d
14 --source $infile 14 --source $infile
15 ## (-m) 15 ## (-m)
16 --model_type $search_model_selector.model_type 16 --model_type $search_model_selector.model_type
17 --base_model $search_model_selector.base_model 17 --base_model $search_model_selector.base_model
18 #if str( $search_model_selector.model_type ) == 'aminoacid': 18 #if str( $search_model_selector.model_type ) == 'aminoacid':
19 #if str( $search_model_selector.aa_model_empirical_base_frequences) == 'true': 19 $search_model_selector.aa_model_empirical_base_frequencies
20 --aa_empirical_freq
21 #end if
22 #if $search_model_selector.aa_search_matrix: 20 #if $search_model_selector.aa_search_matrix:
23 --aa_search_matrix $search_model_selector.aa_search_matrix 21 --aa_search_matrix $search_model_selector.aa_search_matrix
24 #end if 22 #end if
25 #end if 23 #end if
26 ## (-p) 24 ## (-p)
55 ## (-c) 53 ## (-c)
56 #if $selExtraOpts.numofcats: 54 #if $selExtraOpts.numofcats:
57 --numofcats $selExtraOpts.numofcats 55 --numofcats $selExtraOpts.numofcats
58 #end if 56 #end if
59 ## (-d) 57 ## (-d)
60 #if str ($selExtraOpts.search_complete_random_tree) == "true": 58 $selExtraOpts.search_complete_random_tree
61 --search_complete_random_tree
62 #end if
63 ## (-D) 59 ## (-D)
64 #if str ($selExtraOpts.ml_search_convergence) == "true": 60 $selExtraOpts.ml_search_convergence)
65 --ml_search_convergence
66 #end if
67 ## (-e) 61 ## (-e)
68 #if $selExtraOpts.model_opt_precision: 62 #if $selExtraOpts.model_opt_precision:
69 --model_opt_precision $selExtraOpts.model_opt_precision 63 --model_opt_precision $selExtraOpts.model_opt_precision
70 #end if 64 #end if
71 ## (-E) 65 ## (-E)
75 ## (-f) 69 ## (-f)
76 #if $selExtraOpts.search_algorithm: 70 #if $selExtraOpts.search_algorithm:
77 --search_algorithm $selExtraOpts.search_algorithm 71 --search_algorithm $selExtraOpts.search_algorithm
78 #end if 72 #end if
79 ## (-F) 73 ## (-F)
80 #if str ($selExtraOpts.save_memory_cat_model) == "true": 74 $selExtraOpts.save_memory_cat_model
81 --save_memory_cat_model
82 #end if
83 ## (-g) 75 ## (-g)
84 #if $selExtraOpts.groupingfile: 76 #if $selExtraOpts.groupingfile:
85 --groupingfile $selExtraOpts.groupingfile 77 --groupingfile $selExtraOpts.groupingfile
86 #end if 78 #end if
87 ## (-G) 79 ## (-G)
99 ## (-J) 91 ## (-J)
100 #if $selExtraOpts.majority_rule_consensus: 92 #if $selExtraOpts.majority_rule_consensus:
101 --majority_rule_consensus $selExtraOpts.majority_rule_consensus 93 --majority_rule_consensus $selExtraOpts.majority_rule_consensus
102 #end if 94 #end if
103 ## (-k) 95 ## (-k)
104 #if str ($selExtraOpts.print_branch_lengths) == "true": 96 $selExtraOpts.print_branch_lengths
105 --print_branch_lengths
106 #end if
107 ## (-K) 97 ## (-K)
108 #if str ($selExtraOpts.multistate_sub_model) != "": 98 #if str ($selExtraOpts.multistate_sub_model) != "":
109 --multistate_sub_model $selExtraOpts.multistate_sub_model 99 --multistate_sub_model $selExtraOpts.multistate_sub_model
110 #end if 100 #end if
111 ## (-m) - see elsewhere 101 ## (-m) - see elsewhere
112 ## (-M) 102 ## (-M)
113 #if str ($selExtraOpts.estimate_individual_branch_lengths) == "true": 103 $selExtraOpts.estimate_individual_branch_lengths
114 --estimate_individual_branch_lengths
115 #end if
116 ## (-n) - see elsewhere 104 ## (-n) - see elsewhere
117 ## (-o) 105 ## (-o)
118 #if $selExtraOpts.outgroup_name: 106 #if $selExtraOpts.outgroup_name:
119 --outgroup_name $selExtraOpts.outgroup_name 107 --outgroup_name $selExtraOpts.outgroup_name
120 #end if 108 #end if
121 ## (-O) 109 ## (-O)
122 #if str ($selExtraOpts.disable_undetermined_seq_check) == "true": 110 $selExtraOpts.disable_undetermined_seq_check
123 --disable_undetermined_seq_check
124 #end if
125 ## (-P) 111 ## (-P)
126 #if $selExtraOpts.external_protein_model: 112 #if $selExtraOpts.external_protein_model:
127 --external_protein_model $selExtraOpts.external_protein_model 113 --external_protein_model $selExtraOpts.external_protein_model
128 #end if 114 #end if
129 ## (-q) 115 ## (-q)
150 ## (-u) 136 ## (-u)
151 #if str ($selExtraOpts.use_median_approximation) == "true": 137 #if str ($selExtraOpts.use_median_approximation) == "true":
152 --use_median_approximation 138 --use_median_approximation
153 #end if 139 #end if
154 ## (-U) 140 ## (-U)
155 #if str ($selExtraOpts.save_memory_gappy_alignments) == "true": 141 $selExtraOpts.save_memory_gappy_alignments
156 --save_memory_gappy_alignments
157 #end if
158 ## (-V) 142 ## (-V)
159 #if str ($selExtraOpts.disable_rate_heterogeneity) == "true": 143 $selExtraOpts.disable_rate_heterogeneity
160 --disable_rate_heterogeneity
161 #end if
162 ## (-W) 144 ## (-W)
163 #if $selExtraOpts.sliding_window_size: 145 #if $selExtraOpts.sliding_window_size:
164 --sliding_window_size $selExtraOpts.sliding_window_size 146 --sliding_window_size $selExtraOpts.sliding_window_size
165 #end if 147 #end if
166 ## (-x) 148 ## (-x)
167 #if $selExtraOpts.rapid_bootstrap_random_seed: 149 #if $selExtraOpts.rapid_bootstrap_random_seed:
168 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed 150 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
169 #end if 151 #end if
170 ## (-y) 152 ## (-y)
171 #if str ($selExtraOpts.parsimony_starting_tree_only) == "true": 153 $selExtraOpts.parsimony_starting_tree_only)
172 --parsimony_starting_tree_only
173 #end if
174 ## (-z) 154 ## (-z)
175 #if $selExtraOpts.file_multiple_trees: 155 #if $selExtraOpts.file_multiple_trees:
176 --file_multiple_trees $selExtraOpts.file_multiple_trees 156 --file_multiple_trees $selExtraOpts.file_multiple_trees
177 #end if 157 #end if
178 #end if 158 #end if
179 159
180 ##silent sys.stderr.write("DEBUG1 START\n")
181 ##silent sys.stderr.write($selExtraOpts.extraOptions)
182 ##silent sys.stderr.write("\nDEBUG1 END\n")
183
184 </command> 160 </command>
185 <inputs> 161 <inputs>
186 <conditional name="choose_input_type"> 162 ## (-s)
187 <param name="input_type" type="select" label="Input type"> 163 <param type="data" format="fasta,phylip" name="infile" label="Source file"/>
188 <option value="fasta">Fasta</option>
189 <option value="phylip">Phylip</option>
190 </param>
191 ## (-s)
192 <when value="fasta">
193 <param type="data" format="fasta" name="infile" label="Source file"/>
194 </when>
195 <when value="phylip">
196 <param type="data" format="phylip" name="infile" label="Source file"/>
197 </when>
198 </conditional>
199 ## (-m) 164 ## (-m)
200 <conditional name="search_model_selector"> 165 <conditional name="search_model_selector">
201 <param name="model_type" type="select" label="Model Type"> 166 <param name="model_type" type="select" label="Model Type">
202 <option value="nucleotide" selected="true">Nucleotide</option> 167 <option value="nucleotide" selected="true">Nucleotide</option>
203 <option value="aminoacid">Amino Acid</option> 168 <option value="aminoacid">Amino Acid</option>
204 <option value="binary">Binary</option> 169 <option value="binary">Binary</option>
205 <option value="multistate">Multistate</option> 170 <option value="multistate">Multistate</option>
206 </param> 171 </param>
207 <when value="nucleotide"> 172 <when value="nucleotide">
208 ## Nucleotide substitution models 173 ## Nucleotide substitution models
209 <param name="base_model" type="select" label="Substitution Model (-m)"> 174 <param name="base_model" type="select" label="Substitution Model">
210 <option value="GTRCAT">GTRCAT</option> 175 <option value="GTRCAT">GTRCAT</option>
211 <option value="GTRCATI">GTRCATI</option> 176 <option value="GTRCATI">GTRCATI</option>
212 <option value="GTRGAMMA" select="true">GTRGAMMA</option> 177 <option value="GTRGAMMA" select="true">GTRGAMMA</option>
213 <option value="GTRGAMMAI">GTRGAMMAI</option> 178 <option value="GTRGAMMAI">GTRGAMMAI</option>
214 </param> 179 </param>
215 </when> 180 </when>
216 ## Aminoacid substitution models 181 ## Aminoacid substitution models
217 <when value="aminoacid"> 182 <when value="aminoacid">
218 <param name="aa_model_empirical_base_frequences" 183 <param name="aa_model_empirical_base_frequencies"
219 type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use empirical base frequencies in AA models" /> 184 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" />
220 <param name="base_model" type="select" label="Substitution Model (-m)"> 185 <param name="base_model" type="select" label="Substitution Model (-m)">
221 <option value="PROTCAT" select="true">PROTCAT</option> 186 <option value="PROTCAT" select="true">PROTCAT</option>
222 <option value="PROTCATI">PROTCATI</option> 187 <option value="PROTCATI">PROTCATI</option>
223 <option value="PROTGAMMA">PROTGAMMA</option> 188 <option value="PROTGAMMA">PROTGAMMA</option>
224 <option value="PROTGAMMAI">PROTGAMMAI</option> 189 <option value="PROTGAMMAI">PROTGAMMAI</option>
248 <option value="GTR">GTR</option> 213 <option value="GTR">GTR</option>
249 </param> 214 </param>
250 </when> 215 </when>
251 ## Binary substitution models 216 ## Binary substitution models
252 <when value="binary"> 217 <when value="binary">
253 <param name="base_model" type="select" label="Substitution Model (-m)"> 218 <param name="base_model" type="select" label="Substitution Model">
254 <option value="BINCAT">BINCAT</option> 219 <option value="BINCAT">BINCAT</option>
255 <option value="BINCATI">BINCATI</option> 220 <option value="BINCATI">BINCATI</option>
256 <option value="BINGAMMA">BINGAMMA</option> 221 <option value="BINGAMMA">BINGAMMA</option>
257 <option value="BINGAMMAI">BINGAMMAI</option> 222 <option value="BINGAMMAI">BINGAMMAI</option>
258 </param> 223 </param>
259 </when> 224 </when>
260 ## Multi-state substitution models 225 ## Multi-state substitution models
261 <when value="multistate"> 226 <when value="multistate">
262 <param name="base_model" type="select" label="Substitution Model (-m)"> 227 <param name="base_model" type="select" label="Substitution Model">
263 <option value="MULTICAT">MULTICAT</option> 228 <option value="MULTICAT">MULTICAT</option>
264 <option value="MULTICATI">MULTICATI</option> 229 <option value="MULTICATI">MULTICATI</option>
265 <option value="MULTIGAMMA">MULTIGAMMA</option> 230 <option value="MULTIGAMMA">MULTIGAMMA</option>
266 <option value="MULTIGAMMAI">MULTIGAMMAI</option> 231 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
267 </param> 232 </param>
268 </when> 233 </when>
269 </conditional> 234 </conditional>
270 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random 235 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random
271 seed used for the parsimony inferences (-p)" /> 236 seed used for the parsimony inferences" />
272 <conditional name="selExtraOpts"> 237 <conditional name="selExtraOpts">
273 <param name="extraOptions" type="select" label="RAxML options to use" 238 <param name="extraOptions" type="select" label="RAxML options to use"
274 help="The required minimal settings are the input file and the 239 help="The required minimal settings are the input file and the
275 substitution model. To specify extra options select the 'Full option list'"> 240 substitution model. To specify extra options select the 'Full option list'">
276 <option value="required">Required options only</option> 241 <option value="required">Required options only</option>
277 <option value="full">Full option list</option> 242 <option value="full">Full option list</option>
278 </param> 243 </param>
279 <when value="full"> 244 <when value="full">
280 ## (-N/#) 245 ## (-N/#)
281 <param name="number_of_runs" type="integer" size="8" value="" 246 <param name="number_of_runs" type="integer" size="8" value=""
282 label="Number of runs (-N|#)" help="Specify the number of 247 label="Number of runs" help="Specify the number of
283 alternative runs on distinct starting trees In combination 248 alternative runs (-N|#) on distinct starting trees In combination
284 with the '-b' option will invoke a multiple boostrap analysis. 249 with the '-b' option will invoke a multiple boostrap analysis.
285 You can add the bootstopping criteria by choosing the autoMR, 250 You can add the bootstopping criteria by choosing the autoMR,
286 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of 251 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
287 providing a number here. Bootstopping will only work in 252 providing a number here. Bootstopping will only work in
288 combination with '-x' or '-b'." 253 combination with '-x' or '-b'."
289 optional="True" /> 254 optional="True" />
290 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs (-N/#)" optional="True"> 255 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True">
291 <option value="" selected="yes"></option> 256 <option value="" selected="yes"></option>
292 <option value="autoMR">autoMR</option> 257 <option value="autoMR">autoMR</option>
293 <option value="autoMRE">autoMRE</option> 258 <option value="autoMRE">autoMRE</option>
294 <option value="autoMRE_IGN">autoMRE_IGN</option> 259 <option value="autoMRE_IGN">autoMRE_IGN</option>
295 <option value="autoFC">autoFC</option> 260 <option value="autoFC">autoFC</option>
296 </param> 261 </param>
297 ## Alphabetical Listing of Advanced Options 262 ## Alphabetical Listing of Advanced Options
298 ## (-a) 263 ## (-a)
299 <param format="txt" name="weightfile" type="data" label="Column weight file (-a)" optional="True" /> 264 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" />
300 ## (-A) 265 ## (-A)
301 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model (-A)" optional="True"> 266 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True">
302 <option value="" selected="yes"></option> 267 <option value="" selected="yes"></option>
303 <option value="S6A">S6A</option> 268 <option value="S6A">S6A</option>
304 <option value="S6B">S6B</option> 269 <option value="S6B">S6B</option>
305 <option value="S6C">S6C</option> 270 <option value="S6C">S6C</option>
306 <option value="S6D">S6D</option> 271 <option value="S6D">S6D</option>
314 <option value="S16">S16</option> 279 <option value="S16">S16</option>
315 <option value="S16A">S16A</option> 280 <option value="S16A">S16A</option>
316 <option value="S16B">S16B</option> 281 <option value="S16B">S16B</option>
317 </param> 282 </param>
318 ## (-b) 283 ## (-b)
319 <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping (-b)" refresh_on_change='true' optional="True" /> 284 <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true' optional="True" />
320 ## (-x) 285 ## (-x)
321 <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." /> 286 <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." />
322 ## (-B) 287 ## (-B)
323 <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" /> 288 <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" />
324 ## (-c) 289 ## (-c)
325 <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX (-c)" optional="True" /> 290 <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" />
326 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. 291 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now.
327 ## (-d) 292 ## (-d)
328 <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)" /> 293 <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" />
329 ## (-D) 294 ## (-D)
330 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="true" falsevalue="false" label="ML search convergence criterion (-D)" /> 295 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" />
331 ## (-e) 296 ## (-e)
332 <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" /> 297 <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" />
333 ## (-E) 298 ## (-E)
334 <param format="txt" name="excludefile" type="data" label="Exclude file (-E)" optional="True" /> 299 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" />
335 ## (-f) 300 ## (-f)
336 <param name="search_algorithm" type="select" label="Algorithm to execute (-f)" optional="True"> 301 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True">
337 <option value="a">Rapid bootstrap and best ML tree search (a)</option> 302 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
338 <option value="A">Compute marginal ancestral states (A)</option> 303 <option value="A">Compute marginal ancestral states (A)</option>
339 <option value="b">Draw bipartition information (b)</option> 304 <option value="b">Draw bipartition information (b)</option>
340 <option value="c">Check if the alignment can be read (c)</option> 305 <option value="c">Check if the alignment can be read (c)</option>
341 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option> 306 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option>
359 <option value="w">Compute ELW-test on -z trees (w)</option> 324 <option value="w">Compute ELW-test on -z trees (w)</option>
360 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option> 325 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
361 <option value="y">Classify environmental sequences into a reference tree (y)</option> 326 <option value="y">Classify environmental sequences into a reference tree (y)</option>
362 </param> 327 </param>
363 ## (-F) 328 ## (-F)
364 <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" /> 329 <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" />
365 ## (-g) 330 ## (-g)
366 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree (-g)" optional="True" /> 331 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" />
367 ## (-G) 332 ## (-G)
368 <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" > 333 <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" >
369 <validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/> 334 <validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/>
370 </param> 335 </param>
371 ## (-i) 336 ## (-i)
372 <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting (-i)" optional="True" /> 337 <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting" optional="True" />
373 ## (-I) 338 ## (-I)
374 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis (-I)" optional="True"> 339 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True">
375 <option value="" selected="True"></option> 340 <option value="" selected="True"></option>
376 <option value="autoFC">Frequency-based criterion (autoFC)</option> 341 <option value="autoFC">Frequency-based criterion (autoFC)</option>
377 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option> 342 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
378 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option> 343 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
379 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option> 344 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
380 </param> 345 </param>
381 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy 346 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy
382 ## (-J) 347 ## (-J)
383 <param name="majority_rule_consensus" type="select" label="Compute consensus tree (-J)" optional="True"> 348 <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True">
384 <option value="" selected="True"></option> 349 <option value="" selected="True"></option>
385 <option value="MR">Majority-rule consensus tree (MR)</option> 350 <option value="MR">Majority-rule consensus tree (MR)</option>
386 <option value="MRE">Extended majority-rule consensus tree (MRE)</option> 351 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
387 <option value="STRICT">Strict consensus tree (STRICT)</option> 352 <option value="STRICT">Strict consensus tree (STRICT)</option>
388 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option> 353 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
389 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option> 354 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
390 </param> 355 </param>
391 ## (-k) 356 ## (-k)
392 <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" /> 357 <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" />
393 ## (-K) 358 ## (-K)
394 <param name="multistate_sub_model" type="select" label="Specify a 359 <param name="multistate_sub_model" type="select" label="Specify a
395 multi-state substitution model (-K)" optional="True"> 360 multi-state substitution model" optional="True">
396 <option value="" selected="true"></option> 361 <option value="" selected="true"></option>
397 <option value="GTR">GTR</option> 362 <option value="GTR">GTR</option>
398 <option value="ORDERED">ORDERED</option> 363 <option value="ORDERED">ORDERED</option>
399 <option value="MK">MK</option> 364 <option value="MK">MK</option>
400 </param> 365 </param>
401 ## (-M) 366 ## (-M)
402 <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" /> 367 <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" />
403 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files 368 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files
404 ## (-o) 369 ## (-o)
405 <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" /> 370 <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" />
406 ## (-O) 371 ## (-O)
407 <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." /> 372 <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." />
408 <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" /> 373 <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" />
409 ## (-q) 374 ## (-q)
410 <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." /> 375 <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." />
411 ## (-r) 376 ## (-r)
412 <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." /> 377 <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." />
413 ## (-R) 378 ## (-R)
414 <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." /> 379 <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." />
415 ## (-s) source file option is in the required options section 380 ## (-s) source file option is in the required options section
416 ## (-S) 381 ## (-S)
417 <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 '()&lt;&gt;[]{}' to define stem regions and pseudoknots."/> 382 <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."/>
418 ## (-t) 383 ## (-t)
419 <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." /> 384 <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." />
420 ## (-T) is hard-coded in the required options section 385 ## (-T) is hard-coded in the required options section
421 <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" /> 386 <param name="use_median_approximation" type="boolean" checked="no" truevalue="true" falsevalue="false" 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" />
422 ## (-U) 387 ## (-U)
423 <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" /> 388 <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" />
424 ## (-V) 389 ## (-V)
425 <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" /> 390 <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" />
426 ## (-W) 391 ## (-W)
427 <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'" /> 392 <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'" />
428 ## (-x) - see it by the (-b) 393 ## (-x) - see it by the (-b)
429 ## (-y) 394 ## (-y)
430 <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." /> 395 <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." />
431 ## (-z) 396 ## (-z)
432 <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" /> 397 <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" />
433 </when> ## full option list 398 </when> ## full option list
434 </conditional> ## END $selExtraOpts 399 </conditional> ## END $selExtraOpts
435 </inputs> 400 </inputs>
436 <outputs> 401 <outputs>
437 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" /> 402 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />