Mercurial > repos > tiagoantao > raxml
annotate raxml.xml @ 6:2e733a05342f draft
planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty
| author | tiagoantao |
|---|---|
| date | Thu, 22 Oct 2015 18:15:13 -0400 |
| parents | b921c26a1cbc |
| children | 942aa40bd86c |
| rev | line source |
|---|---|
| 0 | 1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1"> |
| 2 <requirements> | |
|
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b4ed83696908
planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty
tiagoantao
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0
diff
changeset
|
3 <requirement type='package' version="8.2.4">raxml</requirement> |
| 0 | 4 </requirements> |
| 5 <description>- Maximum Likelihood based inference of large phylogenetic trees</description> | |
| 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) | |
|
3
b4ed83696908
planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty
tiagoantao
parents:
0
diff
changeset
|
12 --threads \${GALAXY_SLOTS:-1} |
| 0 | 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 #if str( $search_model_selector.aa_model_empirical_base_frequences) == 'true': | |
| 20 --aa_empirical_freq | |
| 21 #end if | |
| 22 #if $search_model_selector.aa_search_matrix: | |
| 23 --aa_search_matrix $search_model_selector.aa_search_matrix | |
| 24 #end if | |
| 25 #end if | |
| 26 ## (-p) | |
| 27 #if $random_seed: | |
| 28 --random_seed $random_seed | |
| 29 #else | |
| 30 --random_seed 1234567890 | |
| 31 #end if | |
| 32 | |
| 33 ## Optional parameters | |
| 34 | |
| 35 #if str( $selExtraOpts.extraOptions ) == 'full': | |
| 36 ## (-N/#) | |
| 37 #if $selExtraOpts.number_of_runs: | |
| 38 --number_of_runs $selExtraOpts.number_of_runs | |
| 39 #end if | |
| 40 #if $selExtraOpts.number_of_runs_bootstop: | |
| 41 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop | |
| 42 #end if | |
| 43 ## (-a) | |
| 44 #if $selExtraOpts.weightfile: | |
| 45 --weightfile $selExtraOpts.weightfile | |
| 46 #end if | |
| 47 ## (-b) | |
| 48 #if str ($selExtraOpts.secondary_structure_model) != "": | |
| 49 --secondary_structure_model $selExtraOpts.secondary_structure_model | |
| 50 #end if | |
| 51 ## (-b) | |
| 52 #if $selExtraOpts.bootseed: | |
| 53 --bootseed $selExtraOpts.bootseed | |
| 54 #end if | |
| 55 ## (-c) | |
| 56 #if $selExtraOpts.numofcats: | |
| 57 --numofcats $selExtraOpts.numofcats | |
| 58 #end if | |
| 59 ## (-d) | |
| 60 #if str ($selExtraOpts.search_complete_random_tree) == "true": | |
| 61 --search_complete_random_tree | |
| 62 #end if | |
| 63 ## (-D) | |
| 64 #if str ($selExtraOpts.ml_search_convergence) == "true": | |
| 65 --ml_search_convergence | |
| 66 #end if | |
| 67 ## (-e) | |
| 68 #if $selExtraOpts.model_opt_precision: | |
| 69 --model_opt_precision $selExtraOpts.model_opt_precision | |
| 70 #end if | |
| 71 ## (-E) | |
| 72 #if $selExtraOpts.excludefile: | |
| 73 --excludefile $selExtraOpts.excludefile | |
| 74 #end if | |
| 75 ## (-f) | |
| 76 #if $selExtraOpts.search_algorithm: | |
| 77 --search_algorithm $selExtraOpts.search_algorithm | |
| 78 #end if | |
| 79 ## (-F) | |
| 80 #if str ($selExtraOpts.save_memory_cat_model) == "true": | |
| 81 --save_memory_cat_model | |
| 82 #end if | |
| 83 ## (-g) | |
| 84 #if $selExtraOpts.groupingfile: | |
| 85 --groupingfile $selExtraOpts.groupingfile | |
| 86 #end if | |
| 87 ## (-G) | |
| 88 #if $selExtraOpts.enable_evol_heuristics: | |
| 89 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics | |
| 90 #end if | |
| 91 ## (-i) | |
| 92 #if $selExtraOpts.initial_rearrangement_setting: | |
| 93 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting | |
| 94 #end if | |
| 95 ## (-I) | |
| 96 #if $selExtraOpts.posterior_bootstopping_analysis: | |
| 97 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis | |
| 98 #end if | |
| 99 ## (-J) | |
| 100 #if $selExtraOpts.majority_rule_consensus: | |
| 101 --majority_rule_consensus $selExtraOpts.majority_rule_consensus | |
| 102 #end if | |
| 103 ## (-k) | |
| 104 #if str ($selExtraOpts.print_branch_lengths) == "true": | |
| 105 --print_branch_lengths | |
| 106 #end if | |
| 107 ## (-K) | |
| 108 #if str ($selExtraOpts.multistate_sub_model) != "": | |
| 109 --multistate_sub_model $selExtraOpts.multistate_sub_model | |
| 110 #end if | |
| 111 ## (-m) - see elsewhere | |
| 112 ## (-M) | |
| 113 #if str ($selExtraOpts.estimate_individual_branch_lengths) == "true": | |
| 114 --estimate_individual_branch_lengths | |
| 115 #end if | |
| 116 ## (-n) - see elsewhere | |
| 117 ## (-o) | |
| 118 #if $selExtraOpts.outgroup_name: | |
| 119 --outgroup_name $selExtraOpts.outgroup_name | |
| 120 #end if | |
| 121 ## (-O) | |
| 122 #if str ($selExtraOpts.disable_undetermined_seq_check) == "true": | |
| 123 --disable_undetermined_seq_check | |
| 124 #end if | |
| 125 ## (-P) | |
| 126 #if $selExtraOpts.external_protein_model: | |
| 127 --external_protein_model $selExtraOpts.external_protein_model | |
| 128 #end if | |
| 129 ## (-q) | |
| 130 #if $selExtraOpts.multiple_model: | |
| 131 --multiple_model $selExtraOpts.multiple_model | |
| 132 #end if | |
| 133 ## (-r) | |
| 134 #if $selExtraOpts.constraint_file: | |
| 135 --constraint_file $selExtraOpts.constraint_file | |
| 136 #end if | |
| 137 ## (-R) | |
| 138 #if $selExtraOpts.bin_model_parameter_file: | |
| 139 --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file | |
| 140 #end if | |
| 141 ## (-S) | |
| 142 #if $selExtraOpts.secondary_structure_file: | |
| 143 --secondary_structure_file $selExtraOpts.secondary_structure_file | |
| 144 #end if | |
| 145 ## (-t) | |
| 146 #if $selExtraOpts.start_tree_file: | |
| 147 --starting_tree $selExtraOpts.start_tree_file | |
| 148 #end if | |
| 149 ## (-T) see elsewhere | |
| 150 ## (-u) | |
| 151 #if str ($selExtraOpts.use_median_approximation) == "true": | |
| 152 --use_median_approximation | |
| 153 #end if | |
| 154 ## (-U) | |
| 155 #if str ($selExtraOpts.save_memory_gappy_alignments) == "true": | |
| 156 --save_memory_gappy_alignments | |
| 157 #end if | |
| 158 ## (-V) | |
| 159 #if str ($selExtraOpts.disable_rate_heterogeneity) == "true": | |
| 160 --disable_rate_heterogeneity | |
| 161 #end if | |
| 162 ## (-W) | |
| 163 #if $selExtraOpts.sliding_window_size: | |
| 164 --sliding_window_size $selExtraOpts.sliding_window_size | |
| 165 #end if | |
| 166 ## (-x) | |
| 167 #if $selExtraOpts.rapid_bootstrap_random_seed: | |
| 168 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed | |
| 169 #end if | |
| 170 ## (-y) | |
| 171 #if str ($selExtraOpts.parsimony_starting_tree_only) == "true": | |
| 172 --parsimony_starting_tree_only | |
| 173 #end if | |
| 174 ## (-z) | |
| 175 #if $selExtraOpts.file_multiple_trees: | |
| 176 --file_multiple_trees $selExtraOpts.file_multiple_trees | |
| 177 #end if | |
| 178 #end if | |
| 179 | |
| 180 ##silent sys.stderr.write("DEBUG1 START\n") | |
| 181 ##silent sys.stderr.write($selExtraOpts.extraOptions) | |
| 182 ##silent sys.stderr.write("\nDEBUG1 END\n") | |
| 183 | |
| 184 </command> | |
| 185 <inputs> | |
| 186 <conditional name="choose_input_type"> | |
| 187 <param name="input_type" type="select" label="Input type"> | |
| 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) | |
| 200 <conditional name="search_model_selector"> | |
| 201 <param name="model_type" type="select" label="Model Type"> | |
| 202 <option value="nucleotide" selected="true">Nucleotide</option> | |
| 203 <option value="aminoacid">Amino Acid</option> | |
| 204 <option value="binary">Binary</option> | |
| 205 <option value="multistate">Multistate</option> | |
| 206 </param> | |
| 207 <when value="nucleotide"> | |
| 208 ## Nucleotide substitution models | |
| 209 <param name="base_model" type="select" label="Substitution Model (-m)"> | |
| 210 <option value="GTRCAT">GTRCAT</option> | |
| 211 <option value="GTRCATI">GTRCATI</option> | |
| 212 <option value="GTRGAMMA" select="true">GTRGAMMA</option> | |
| 213 <option value="GTRGAMMAI">GTRGAMMAI</option> | |
| 214 </param> | |
| 215 </when> | |
| 216 ## Aminoacid substitution models | |
| 217 <when value="aminoacid"> | |
| 218 <param name="aa_model_empirical_base_frequences" | |
| 219 type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use empirical base frequencies in AA models" /> | |
| 220 <param name="base_model" type="select" label="Substitution Model (-m)"> | |
| 221 <option value="PROTCAT" select="true">PROTCAT</option> | |
| 222 <option value="PROTCATI">PROTCATI</option> | |
| 223 <option value="PROTGAMMA">PROTGAMMA</option> | |
| 224 <option value="PROTGAMMAI">PROTGAMMAI</option> | |
| 225 </param> | |
| 226 <param name="aa_search_matrix" type="select" label="Matrix"> | |
| 227 <option value="DAYHOFF" select="true">DAYHOFF</option> | |
| 228 <option value="DCMUT">DCMUT</option> | |
| 229 <option value="JTT">JTT</option> | |
| 230 <option value="MTREV">MTREV</option> | |
| 231 <option value="WAG">WAG</option> | |
| 232 <option value="RTREV">RTREV</option> | |
| 233 <option value="CPREV">CPREV</option> | |
| 234 <option value="VT">VT</option> | |
| 235 <option value="BLOSUM62">BLOSUM62</option> | |
| 236 <option value="MTMAM">MTMAM</option> | |
| 237 <option value="LG">LG</option> | |
| 238 <option value="MTART">MTART</option> | |
| 239 <option value="MTZOA">MTZOA</option> | |
| 240 <option value="PMB">PMB</option> | |
| 241 <option value="HIVB">HIVB</option> | |
| 242 <option value="HIVW">HIVW</option> | |
| 243 <option value="JTTDCMUT">JTTDCMUT</option> | |
| 244 <option value="FLU">FLU</option> | |
| 245 <option value="DUMMY">DUMMY</option> | |
| 246 <option value="DUMMY2">DUMMY2</option> | |
| 247 <option value="GTR_UNLINKED">GTR_UNLINKED</option> | |
| 248 <option value="GTR">GTR</option> | |
| 249 </param> | |
| 250 </when> | |
| 251 ## Binary substitution models | |
| 252 <when value="binary"> | |
| 253 <param name="base_model" type="select" label="Substitution Model (-m)"> | |
| 254 <option value="BINCAT">BINCAT</option> | |
| 255 <option value="BINCATI">BINCATI</option> | |
| 256 <option value="BINGAMMA">BINGAMMA</option> | |
| 257 <option value="BINGAMMAI">BINGAMMAI</option> | |
| 258 </param> | |
| 259 </when> | |
| 260 ## Multi-state substitution models | |
| 261 <when value="multistate"> | |
| 262 <param name="base_model" type="select" label="Substitution Model (-m)"> | |
| 263 <option value="MULTICAT">MULTICAT</option> | |
| 264 <option value="MULTICATI">MULTICATI</option> | |
| 265 <option value="MULTIGAMMA">MULTIGAMMA</option> | |
| 266 <option value="MULTIGAMMAI">MULTIGAMMAI</option> | |
| 267 </param> | |
| 268 </when> | |
| 269 </conditional> | |
| 270 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random | |
| 271 seed used for the parsimony inferences (-p)" /> | |
| 272 <conditional name="selExtraOpts"> | |
| 273 <param name="extraOptions" type="select" label="RAxML options to use" | |
| 274 help="The required minimal settings are the input file and the | |
| 275 substitution model. To specify extra options select the 'Full option list'"> | |
| 276 <option value="required">Required options only</option> | |
| 277 <option value="full">Full option list</option> | |
| 278 </param> | |
| 279 <when value="full"> | |
| 280 ## (-N/#) | |
| 281 <param name="number_of_runs" type="integer" size="8" value="" | |
| 282 label="Number of runs (-N|#)" help="Specify the number of | |
| 283 alternative runs on distinct starting trees In combination | |
| 284 with the '-b' option will invoke a multiple boostrap analysis. | |
| 285 You can add the bootstopping criteria by choosing the autoMR, | |
| 286 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of | |
| 287 providing a number here. Bootstopping will only work in | |
| 288 combination with '-x' or '-b'." | |
| 289 optional="True" /> | |
| 290 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs (-N/#)" optional="True"> | |
| 291 <option value="" selected="yes"></option> | |
| 292 <option value="autoMR">autoMR</option> | |
| 293 <option value="autoMRE">autoMRE</option> | |
| 294 <option value="autoMRE_IGN">autoMRE_IGN</option> | |
| 295 <option value="autoFC">autoFC</option> | |
| 296 </param> | |
| 297 ## Alphabetical Listing of Advanced Options | |
| 298 ## (-a) | |
| 299 <param format="txt" name="weightfile" type="data" label="Column weight file (-a)" optional="True" /> | |
| 300 ## (-A) | |
| 301 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model (-A)" optional="True"> | |
| 302 <option value="" selected="yes"></option> | |
| 303 <option value="S6A">S6A</option> | |
| 304 <option value="S6B">S6B</option> | |
| 305 <option value="S6C">S6C</option> | |
| 306 <option value="S6D">S6D</option> | |
| 307 <option value="S6E">S6E</option> | |
| 308 <option value="S7A">S7A</option> | |
| 309 <option value="S7B">S7B</option> | |
| 310 <option value="S7C">S7C</option> | |
| 311 <option value="S7D">S7D</option> | |
| 312 <option value="S7E">S7E</option> | |
| 313 <option value="S7F">S7F</option> | |
| 314 <option value="S16">S16</option> | |
| 315 <option value="S16A">S16A</option> | |
| 316 <option value="S16B">S16B</option> | |
| 317 </param> | |
| 318 ## (-b) | |
| 319 <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping (-b)" refresh_on_change='true' optional="True" /> | |
| 320 ## (-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." /> | |
| 322 ## (-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" /> | |
| 324 ## (-c) | |
| 325 <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX (-c)" optional="True" /> | |
| 326 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. | |
| 327 ## (-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)" /> | |
| 329 ## (-D) | |
| 330 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="true" falsevalue="false" label="ML search convergence criterion (-D)" /> | |
| 331 ## (-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" /> | |
| 333 ## (-E) | |
| 334 <param format="txt" name="excludefile" type="data" label="Exclude file (-E)" optional="True" /> | |
| 335 ## (-f) | |
| 336 <param name="search_algorithm" type="select" label="Algorithm to execute (-f)" optional="True"> | |
| 337 <option value="a">Rapid bootstrap and best ML tree search (a)</option> | |
| 338 <option value="A">Compute marginal ancestral states (A)</option> | |
| 339 <option value="b">Draw bipartition information (b)</option> | |
| 340 <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> | |
| 342 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option> | |
| 343 <option value="g">Compute per-site log likelihoods for -z trees (g)</option> | |
| 344 <option value="h">Compute log likelihood test for -t / -z trees (h)</option> | |
| 345 <option value="j">Generate bootstrapped alignment files (j)</option> | |
| 346 <option value="J">Compute SH-like support values for the -t tree (J)</option> | |
| 347 <option value="m">Compare bipartitions between -t and -z trees (m)</option> | |
| 348 <option value="n">Compute log likelihood score for -z trees (n)</option> | |
| 349 <option value="o">Use old slower search algorithm (o)</option> | |
| 350 <option value="p">Stepwise MP addition of new sequences (p)</option> | |
| 351 <option value="q">Fast quartet calculator (q)</option> | |
| 352 <option value="r">Compute pairwise RF distances in -z trees (r)</option> | |
| 353 <option value="s">Split a multi-gene alignment (s)</option> | |
| 354 <option value="S">Compute site-specific placement bias (S)</option> | |
| 355 <option value="t">Randomized tree searches on a fixed starting tree (t)</option> | |
| 356 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option> | |
| 357 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option> | |
| 358 <option value="v">Classify environmental sequences (v)</option> | |
| 359 <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> | |
| 361 <option value="y">Classify environmental sequences into a reference tree (y)</option> | |
| 362 </param> | |
| 363 ## (-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" /> | |
| 365 ## (-g) | |
| 366 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree (-g)" optional="True" /> | |
| 367 ## (-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" > | |
| 369 <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/> | |
| 370 </param> | |
| 371 ## (-i) | |
| 372 <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting (-i)" optional="True" /> | |
| 373 ## (-I) | |
| 374 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis (-I)" optional="True"> | |
| 375 <option value="" selected="True"></option> | |
| 376 <option value="autoFC">Frequency-based criterion (autoFC)</option> | |
| 377 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option> | |
| 378 <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> | |
| 380 </param> | |
| 381 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy | |
| 382 ## (-J) | |
| 383 <param name="majority_rule_consensus" type="select" label="Compute consensus tree (-J)" optional="True"> | |
| 384 <option value="" selected="True"></option> | |
| 385 <option value="MR">Majority-rule consensus tree (MR)</option> | |
| 386 <option value="MRE">Extended majority-rule consensus tree (MRE)</option> | |
| 387 <option value="STRICT">Strict consensus tree (STRICT)</option> | |
| 388 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option> | |
| 389 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option> | |
| 390 </param> | |
| 391 ## (-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" /> | |
| 393 ## (-K) | |
| 394 <param name="multistate_sub_model" type="select" label="Specify a | |
| 395 multi-state substitution model (-K)" optional="True"> | |
| 396 <option value="" selected="true"></option> | |
| 397 <option value="GTR">GTR</option> | |
| 398 <option value="ORDERED">ORDERED</option> | |
| 399 <option value="MK">MK</option> | |
| 400 </param> | |
| 401 ## (-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" /> | |
| 403 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files | |
| 404 ## (-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" /> | |
| 406 ## (-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." /> | |
| 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" /> | |
| 409 ## (-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." /> | |
| 411 ## (-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." /> | |
| 413 ## (-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." /> | |
| 415 ## (-s) source file option is in the required options section | |
| 416 ## (-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 '()<>[]{}' to define stem regions and pseudoknots."/> | |
| 418 ## (-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." /> | |
| 420 ## (-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" /> | |
| 422 ## (-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" /> | |
| 424 ## (-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" /> | |
| 426 ## (-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'" /> | |
| 428 ## (-x) - see it by the (-b) | |
| 429 ## (-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." /> | |
| 431 ## (-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" /> | |
| 433 </when> ## full option list | |
| 434 </conditional> ## END $selExtraOpts | |
| 435 </inputs> | |
| 436 <outputs> | |
| 437 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" /> | |
| 438 ## REQUIRED | |
| 439 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log"> | |
| 440 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> | |
| 441 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 442 </data> | |
| 443 <data format="txt" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> | |
| 444 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> | |
| 445 </data> | |
| 446 <data format="txt" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> | |
| 447 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> | |
| 448 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 449 </data> | |
| 450 <data format="txt" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result"> | |
| 451 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> | |
| 452 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 453 </data> | |
| 454 ## ADVANCED | |
| 455 <data format="txt" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree"> | |
| 456 <filter>selExtraOpts['search_complete_random_tree'] is True</filter> | |
| 457 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 458 </data> | |
| 459 <data format="txt" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> | |
| 460 <filter>(selExtraOpts['extraOptions'] == 'full')</filter> | |
| 461 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '' or selExtraOpts['bootseed'] == '') and (selExtraOpts['search_algorithm'] == 'a')</filter> | |
| 462 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> | |
| 463 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter> | |
| 464 </data> | |
| 465 <data format="txt" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> | |
| 466 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 467 <filter>(selExtraOpts['multiple_model'] != '')</filter> | |
| 468 </data> | |
| 469 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions"> | |
| 470 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 471 <filter>selExtraOpts['multiple_model'] is not None </filter> | |
| 472 </data> | |
| 473 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log"> | |
| 474 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 475 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 476 <filter>(selExtraOpts['bootseed'] == '')</filter> | |
| 477 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> | |
| 478 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> | |
| 479 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 480 </data> | |
| 481 <data format="txt" name="result" from_work_dir="RAxML_result.galaxy" label="Result"> | |
| 482 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 483 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 484 <filter>selExtraOpts['bootseed'] == ''</filter> | |
| 485 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 486 <filter>selExtraOpts['search_algorithm'] != 'b'</filter> | |
| 487 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 488 </data> | |
| 489 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions"> | |
| 490 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 491 <filter>(selExtraOpts['multiple_model'] is not None)</filter> | |
| 492 </data> | |
| 493 <data format="txt" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> | |
| 494 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 495 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 496 <filter>(selExtraOpts['bootseed'] == '')</filter> | |
| 497 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> | |
| 498 <filter>(selExtraOpts['constraint_file'] is None)</filter> | |
| 499 <filter>(selExtraOpts['groupingfile'] is None)</filter> | |
| 500 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter> | |
| 501 <filter>(selExtraOpts['start_tree_file'] is None)</filter> | |
| 502 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 503 </data> | |
| 504 <data format="txt" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees"> | |
| 505 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 506 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter> | |
| 507 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter> | |
| 508 </data> | |
| 509 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions"> | |
| 510 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> | |
| 511 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 512 </data> | |
| 513 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels"> | |
| 514 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 515 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> | |
| 516 </data> | |
| 517 <data format="txt" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree"> | |
| 518 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 519 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter> | |
| 520 </data> | |
| 521 <data format="txt" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree"> | |
| 522 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 523 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter> | |
| 524 </data> | |
| 525 <data format="txt" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree"> | |
| 526 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 527 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter> | |
| 528 </data> | |
| 529 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences."> | |
| 530 <filter>selExtraOpts['search_algorithm'] == 'm' </filter> | |
| 531 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 532 </data> | |
| 533 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores"> | |
| 534 <filter>selExtraOpts['search_algorithm'] == 'g' </filter> | |
| 535 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 536 </data> | |
| 537 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances"> | |
| 538 <filter>selExtraOpts['search_algorithm'] == 'x' </filter> | |
| 539 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 540 </data> | |
| 541 </outputs> | |
| 542 <tests> | |
| 543 <test> | |
| 544 <param name="extraOptions" value="required"/> | |
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545 <param name="infile" value="test-data/dna.phy"/> |
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546 <param name="model_type" value="nucleotide"/> |
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547 <param name="base_model" value="GTRCAT"/> |
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548 <output name="bestTreeReq" file="RAxML_bestTree.galaxy"/> |
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549 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy"/> |
| 0 | 550 <!-- <output name="info" file="raxml/test1/RAxML_info.galaxy"/> --> |
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551 <output name="logReq" file="RAxML_log.galaxy"> |
| 0 | 552 <assert_contents> |
| 553 <has_line_matching expression="^0\\..*" /> | |
| 554 </assert_contents> | |
| 555 </output> | |
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556 <output name="resultReq" file="RAxML_result.galaxy"> |
| 0 | 557 <assert_contents> |
| 558 <has_line_matching expression="Overall\sexecution\stime.*" /> | |
| 559 </assert_contents> | |
| 560 </output> | |
| 561 </test> | |
| 562 </tests> | |
| 563 <help> | |
| 564 Title: | |
| 565 ______ | |
| 566 Randomized Axelerated Maximum Likelihood | |
| 567 | |
| 568 Author: | |
| 569 _______ | |
| 570 Alexandros Stamatakis <alexandros.stamatakis@h-its.org> | |
| 571 | |
| 572 Description: | |
| 573 ____________ | |
| 574 | |
| 575 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic | |
| 576 trees. The program is explicitly being developed to efficiently infer trees for | |
| 577 extremely large datasets, either in terms of the number of taxa and/or the | |
| 578 sequence length. | |
| 579 | |
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580 This wrapper works with the RAxML version 8.2.4. |
| 0 | 581 |
| 582 URL: | |
| 583 ____ | |
| 584 Author's page: http://www.exelixis-lab.org/ | |
| 585 | |
| 586 Help: http://groups.google.com/group/raxml | |
| 587 | |
| 588 | |
| 589 Tool development: | |
| 590 ----------------- | |
| 591 Oleksandr Moskalenko with adaptations from Tiago Antao. | |
| 592 | |
| 593 </help> | |
| 594 <citations> | |
| 595 <citation type="doi">10.1093/bioinformatics/btu033</citation> | |
| 596 <citation type="bibtex"> | |
| 597 @article{stamatakis2014raxml, | |
| 598 title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies}, | |
| 599 author={Stamatakis, Alexandros}, | |
| 600 journal={Bioinformatics}, | |
| 601 volume={30}, | |
| 602 number={9}, | |
| 603 pages={1312--1313}, | |
| 604 year={2014}, | |
| 605 publisher={Oxford Univ Press}} | |
| 606 </citation> | |
| 607 </citations> | |
| 608 </tool> |