Mercurial > repos > tiagoantao > raxml
annotate raxml.xml @ 26:efe9ed0d5c4a draft
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| author | tiagoantao |
|---|---|
| date | Fri, 13 Nov 2015 09:32:12 -0500 |
| parents | 2d9f1ef9b5cc |
| children | c73243ef3476 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1"> |
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2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description> |
| 0 | 3 <requirements> |
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4 <requirement type='package' version="8.2.4">raxml</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python">raxml.py | |
| 7 ## Required parameters | |
| 8 ## binary is hard-coded to the pthreads enabled raxml executable | |
| 9 --binary "raxmlHPC-PTHREADS" | |
| 10 ## (-T) | |
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11 #if GALAXY_SLOTS != 1: |
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12 --threads $GALAXY_SLOTS |
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13 #end if |
| 0 | 14 ## (-s) |
| 15 --source $infile | |
| 16 ## (-m) | |
| 17 --model_type $search_model_selector.model_type | |
| 18 --base_model $search_model_selector.base_model | |
| 19 #if str( $search_model_selector.model_type ) == 'aminoacid': | |
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20 $search_model_selector.aa_model_empirical_base_frequencies |
| 0 | 21 #if $search_model_selector.aa_search_matrix: |
| 22 --aa_search_matrix $search_model_selector.aa_search_matrix | |
| 23 #end if | |
| 24 #end if | |
| 25 ## (-p) | |
| 26 #if $random_seed: | |
| 27 --random_seed $random_seed | |
| 28 #else | |
| 29 --random_seed 1234567890 | |
| 30 #end if | |
| 31 | |
| 32 ## Optional parameters | |
| 33 | |
| 34 #if str( $selExtraOpts.extraOptions ) == 'full': | |
| 35 ## (-N/#) | |
| 36 #if $selExtraOpts.number_of_runs: | |
| 37 --number_of_runs $selExtraOpts.number_of_runs | |
| 38 #end if | |
| 39 #if $selExtraOpts.number_of_runs_bootstop: | |
| 40 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop | |
| 41 #end if | |
| 42 ## (-a) | |
| 43 #if $selExtraOpts.weightfile: | |
| 44 --weightfile $selExtraOpts.weightfile | |
| 45 #end if | |
| 46 ## (-b) | |
| 47 #if str ($selExtraOpts.secondary_structure_model) != "": | |
| 48 --secondary_structure_model $selExtraOpts.secondary_structure_model | |
| 49 #end if | |
| 50 ## (-b) | |
| 51 #if $selExtraOpts.bootseed: | |
| 52 --bootseed $selExtraOpts.bootseed | |
| 53 #end if | |
| 54 ## (-c) | |
| 55 #if $selExtraOpts.numofcats: | |
| 56 --numofcats $selExtraOpts.numofcats | |
| 57 #end if | |
| 58 ## (-d) | |
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59 $selExtraOpts.search_complete_random_tree |
| 0 | 60 ## (-D) |
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61 $selExtraOpts.ml_search_convergence |
| 0 | 62 ## (-e) |
| 63 #if $selExtraOpts.model_opt_precision: | |
| 64 --model_opt_precision $selExtraOpts.model_opt_precision | |
| 65 #end if | |
| 66 ## (-E) | |
| 67 #if $selExtraOpts.excludefile: | |
| 68 --excludefile $selExtraOpts.excludefile | |
| 69 #end if | |
| 70 ## (-f) | |
| 71 #if $selExtraOpts.search_algorithm: | |
| 72 --search_algorithm $selExtraOpts.search_algorithm | |
| 73 #end if | |
| 74 ## (-F) | |
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75 $selExtraOpts.save_memory_cat_model |
| 0 | 76 ## (-g) |
| 77 #if $selExtraOpts.groupingfile: | |
| 78 --groupingfile $selExtraOpts.groupingfile | |
| 79 #end if | |
| 80 ## (-G) | |
| 81 #if $selExtraOpts.enable_evol_heuristics: | |
| 82 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics | |
| 83 #end if | |
| 84 ## (-i) | |
| 85 #if $selExtraOpts.initial_rearrangement_setting: | |
| 86 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting | |
| 87 #end if | |
| 88 ## (-I) | |
| 89 #if $selExtraOpts.posterior_bootstopping_analysis: | |
| 90 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis | |
| 91 #end if | |
| 92 ## (-J) | |
| 93 #if $selExtraOpts.majority_rule_consensus: | |
| 94 --majority_rule_consensus $selExtraOpts.majority_rule_consensus | |
| 95 #end if | |
| 96 ## (-k) | |
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97 $selExtraOpts.print_branch_lengths |
| 0 | 98 ## (-K) |
| 99 #if str ($selExtraOpts.multistate_sub_model) != "": | |
| 100 --multistate_sub_model $selExtraOpts.multistate_sub_model | |
| 101 #end if | |
| 102 ## (-m) - see elsewhere | |
| 103 ## (-M) | |
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104 $selExtraOpts.estimate_individual_branch_lengths |
| 0 | 105 ## (-n) - see elsewhere |
| 106 ## (-o) | |
| 107 #if $selExtraOpts.outgroup_name: | |
| 108 --outgroup_name $selExtraOpts.outgroup_name | |
| 109 #end if | |
| 110 ## (-O) | |
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111 $selExtraOpts.disable_undetermined_seq_check |
| 0 | 112 ## (-P) |
| 113 #if $selExtraOpts.external_protein_model: | |
| 114 --external_protein_model $selExtraOpts.external_protein_model | |
| 115 #end if | |
| 116 ## (-q) | |
| 117 #if $selExtraOpts.multiple_model: | |
| 118 --multiple_model $selExtraOpts.multiple_model | |
| 119 #end if | |
| 120 ## (-r) | |
| 121 #if $selExtraOpts.constraint_file: | |
| 122 --constraint_file $selExtraOpts.constraint_file | |
| 123 #end if | |
| 124 ## (-R) | |
| 125 #if $selExtraOpts.bin_model_parameter_file: | |
| 126 --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file | |
| 127 #end if | |
| 128 ## (-S) | |
| 129 #if $selExtraOpts.secondary_structure_file: | |
| 130 --secondary_structure_file $selExtraOpts.secondary_structure_file | |
| 131 #end if | |
| 132 ## (-t) | |
| 133 #if $selExtraOpts.start_tree_file: | |
| 134 --starting_tree $selExtraOpts.start_tree_file | |
| 135 #end if | |
| 136 ## (-T) see elsewhere | |
| 137 ## (-u) | |
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138 $selExtraOpts.use_median_approximation |
| 0 | 139 ## (-U) |
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140 $selExtraOpts.save_memory_gappy_alignments |
| 0 | 141 ## (-V) |
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142 $selExtraOpts.disable_rate_heterogeneity |
| 0 | 143 ## (-W) |
| 144 #if $selExtraOpts.sliding_window_size: | |
| 145 --sliding_window_size $selExtraOpts.sliding_window_size | |
| 146 #end if | |
| 147 ## (-x) | |
| 148 #if $selExtraOpts.rapid_bootstrap_random_seed: | |
| 149 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed | |
| 150 #end if | |
| 151 ## (-y) | |
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152 $selExtraOpts.parsimony_starting_tree_only |
| 0 | 153 ## (-z) |
| 154 #if $selExtraOpts.file_multiple_trees: | |
| 155 --file_multiple_trees $selExtraOpts.file_multiple_trees | |
| 156 #end if | |
| 157 #end if | |
| 158 | |
| 159 </command> | |
| 160 <inputs> | |
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161 ## (-s) |
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162 <param type="data" format="fasta,phylip" name="infile" label="Source file"/> |
| 0 | 163 ## (-m) |
| 164 <conditional name="search_model_selector"> | |
| 165 <param name="model_type" type="select" label="Model Type"> | |
| 166 <option value="nucleotide" selected="true">Nucleotide</option> | |
| 167 <option value="aminoacid">Amino Acid</option> | |
| 168 <option value="binary">Binary</option> | |
| 169 <option value="multistate">Multistate</option> | |
| 170 </param> | |
| 171 <when value="nucleotide"> | |
| 172 ## Nucleotide substitution models | |
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173 <param name="base_model" type="select" label="Substitution Model"> |
| 0 | 174 <option value="GTRCAT">GTRCAT</option> |
| 175 <option value="GTRCATI">GTRCATI</option> | |
| 176 <option value="GTRGAMMA" select="true">GTRGAMMA</option> | |
| 177 <option value="GTRGAMMAI">GTRGAMMAI</option> | |
| 178 </param> | |
| 179 </when> | |
| 180 ## Aminoacid substitution models | |
| 181 <when value="aminoacid"> | |
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182 <param name="aa_model_empirical_base_frequencies" |
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183 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" /> |
| 0 | 184 <param name="base_model" type="select" label="Substitution Model (-m)"> |
| 185 <option value="PROTCAT" select="true">PROTCAT</option> | |
| 186 <option value="PROTCATI">PROTCATI</option> | |
| 187 <option value="PROTGAMMA">PROTGAMMA</option> | |
| 188 <option value="PROTGAMMAI">PROTGAMMAI</option> | |
| 189 </param> | |
| 190 <param name="aa_search_matrix" type="select" label="Matrix"> | |
| 191 <option value="DAYHOFF" select="true">DAYHOFF</option> | |
| 192 <option value="DCMUT">DCMUT</option> | |
| 193 <option value="JTT">JTT</option> | |
| 194 <option value="MTREV">MTREV</option> | |
| 195 <option value="WAG">WAG</option> | |
| 196 <option value="RTREV">RTREV</option> | |
| 197 <option value="CPREV">CPREV</option> | |
| 198 <option value="VT">VT</option> | |
| 199 <option value="BLOSUM62">BLOSUM62</option> | |
| 200 <option value="MTMAM">MTMAM</option> | |
| 201 <option value="LG">LG</option> | |
| 202 <option value="MTART">MTART</option> | |
| 203 <option value="MTZOA">MTZOA</option> | |
| 204 <option value="PMB">PMB</option> | |
| 205 <option value="HIVB">HIVB</option> | |
| 206 <option value="HIVW">HIVW</option> | |
| 207 <option value="JTTDCMUT">JTTDCMUT</option> | |
| 208 <option value="FLU">FLU</option> | |
| 209 <option value="DUMMY">DUMMY</option> | |
| 210 <option value="DUMMY2">DUMMY2</option> | |
| 211 <option value="GTR_UNLINKED">GTR_UNLINKED</option> | |
| 212 <option value="GTR">GTR</option> | |
| 213 </param> | |
| 214 </when> | |
| 215 ## Binary substitution models | |
| 216 <when value="binary"> | |
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217 <param name="base_model" type="select" label="Substitution Model"> |
| 0 | 218 <option value="BINCAT">BINCAT</option> |
| 219 <option value="BINCATI">BINCATI</option> | |
| 220 <option value="BINGAMMA">BINGAMMA</option> | |
| 221 <option value="BINGAMMAI">BINGAMMAI</option> | |
| 222 </param> | |
| 223 </when> | |
| 224 ## Multi-state substitution models | |
| 225 <when value="multistate"> | |
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226 <param name="base_model" type="select" label="Substitution Model"> |
| 0 | 227 <option value="MULTICAT">MULTICAT</option> |
| 228 <option value="MULTICATI">MULTICATI</option> | |
| 229 <option value="MULTIGAMMA">MULTIGAMMA</option> | |
| 230 <option value="MULTIGAMMAI">MULTIGAMMAI</option> | |
| 231 </param> | |
| 232 </when> | |
| 233 </conditional> | |
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234 <param name="random_seed" type="integer" value="1234567890" label="Random |
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235 seed used for the parsimony inferences" /> |
| 0 | 236 <conditional name="selExtraOpts"> |
| 237 <param name="extraOptions" type="select" label="RAxML options to use" | |
| 238 help="The required minimal settings are the input file and the | |
| 239 substitution model. To specify extra options select the 'Full option list'"> | |
| 240 <option value="required">Required options only</option> | |
| 241 <option value="full">Full option list</option> | |
| 242 </param> | |
| 243 <when value="full"> | |
| 244 ## (-N/#) | |
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245 <param name="number_of_runs" type="integer" value="" |
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246 label="Number of runs" help="Specify the number of |
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247 alternative runs (-N|#) on distinct starting trees In combination |
| 0 | 248 with the '-b' option will invoke a multiple boostrap analysis. |
| 249 You can add the bootstopping criteria by choosing the autoMR, | |
| 250 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of | |
| 251 providing a number here. Bootstopping will only work in | |
| 252 combination with '-x' or '-b'." | |
| 253 optional="True" /> | |
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254 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True"> |
| 0 | 255 <option value="" selected="yes"></option> |
| 256 <option value="autoMR">autoMR</option> | |
| 257 <option value="autoMRE">autoMRE</option> | |
| 258 <option value="autoMRE_IGN">autoMRE_IGN</option> | |
| 259 <option value="autoFC">autoFC</option> | |
| 260 </param> | |
| 261 ## Alphabetical Listing of Advanced Options | |
| 262 ## (-a) | |
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263 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" /> |
| 0 | 264 ## (-A) |
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265 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True"> |
| 0 | 266 <option value="" selected="yes"></option> |
| 267 <option value="S6A">S6A</option> | |
| 268 <option value="S6B">S6B</option> | |
| 269 <option value="S6C">S6C</option> | |
| 270 <option value="S6D">S6D</option> | |
| 271 <option value="S6E">S6E</option> | |
| 272 <option value="S7A">S7A</option> | |
| 273 <option value="S7B">S7B</option> | |
| 274 <option value="S7C">S7C</option> | |
| 275 <option value="S7D">S7D</option> | |
| 276 <option value="S7E">S7E</option> | |
| 277 <option value="S7F">S7F</option> | |
| 278 <option value="S16">S16</option> | |
| 279 <option value="S16A">S16A</option> | |
| 280 <option value="S16B">S16B</option> | |
| 281 </param> | |
| 282 ## (-b) | |
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283 <param name="bootseed" type="integer" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true' optional="True" /> |
| 0 | 284 ## (-x) |
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285 <param name="rapid_bootstrap_random_seed" type="integer" value='' 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." /> |
| 0 | 286 ## (-B) |
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287 <param name="cutoff_threshold" type="float" label="MR Cutoff threshold" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" /> |
| 0 | 288 ## (-c) |
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289 <param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" /> |
| 0 | 290 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. |
| 291 ## (-d) | |
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292 <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" /> |
| 0 | 293 ## (-D) |
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294 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" /> |
| 0 | 295 ## (-e) |
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296 <param name="model_opt_precision" type="float" 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" /> |
| 0 | 297 ## (-E) |
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298 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" /> |
| 0 | 299 ## (-f) |
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300 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True"> |
| 0 | 301 <option value="a">Rapid bootstrap and best ML tree search (a)</option> |
| 302 <option value="A">Compute marginal ancestral states (A)</option> | |
| 303 <option value="b">Draw bipartition information (b)</option> | |
| 304 <option value="c">Check if the alignment can be read (c)</option> | |
| 305 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option> | |
| 306 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option> | |
| 307 <option value="g">Compute per-site log likelihoods for -z trees (g)</option> | |
| 308 <option value="h">Compute log likelihood test for -t / -z trees (h)</option> | |
| 309 <option value="j">Generate bootstrapped alignment files (j)</option> | |
| 310 <option value="J">Compute SH-like support values for the -t tree (J)</option> | |
| 311 <option value="m">Compare bipartitions between -t and -z trees (m)</option> | |
| 312 <option value="n">Compute log likelihood score for -z trees (n)</option> | |
| 313 <option value="o">Use old slower search algorithm (o)</option> | |
| 314 <option value="p">Stepwise MP addition of new sequences (p)</option> | |
| 315 <option value="q">Fast quartet calculator (q)</option> | |
| 316 <option value="r">Compute pairwise RF distances in -z trees (r)</option> | |
| 317 <option value="s">Split a multi-gene alignment (s)</option> | |
| 318 <option value="S">Compute site-specific placement bias (S)</option> | |
| 319 <option value="t">Randomized tree searches on a fixed starting tree (t)</option> | |
| 320 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option> | |
| 321 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option> | |
| 322 <option value="v">Classify environmental sequences (v)</option> | |
| 323 <option value="w">Compute ELW-test on -z trees (w)</option> | |
| 324 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option> | |
| 325 <option value="y">Classify environmental sequences into a reference tree (y)</option> | |
| 326 </param> | |
| 327 ## (-F) | |
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328 <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" /> |
| 0 | 329 ## (-g) |
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330 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" /> |
| 0 | 331 ## (-G) |
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332 <param name="enable_evol_heuristics" type="float" 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" > |
| 0 | 333 <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/> |
| 334 </param> | |
| 335 ## (-i) | |
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336 <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" /> |
| 0 | 337 ## (-I) |
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338 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True"> |
| 0 | 339 <option value="" selected="True"></option> |
| 340 <option value="autoFC">Frequency-based criterion (autoFC)</option> | |
| 341 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option> | |
| 342 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option> | |
| 343 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option> | |
| 344 </param> | |
| 345 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy | |
| 346 ## (-J) | |
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347 <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True"> |
| 0 | 348 <option value="" selected="True"></option> |
| 349 <option value="MR">Majority-rule consensus tree (MR)</option> | |
| 350 <option value="MRE">Extended majority-rule consensus tree (MRE)</option> | |
| 351 <option value="STRICT">Strict consensus tree (STRICT)</option> | |
| 352 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option> | |
| 353 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option> | |
| 354 </param> | |
| 355 ## (-k) | |
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356 <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" /> |
| 0 | 357 ## (-K) |
| 358 <param name="multistate_sub_model" type="select" label="Specify a | |
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359 multi-state substitution model" optional="True"> |
| 0 | 360 <option value="" selected="true"></option> |
| 361 <option value="GTR">GTR</option> | |
| 362 <option value="ORDERED">ORDERED</option> | |
| 363 <option value="MK">MK</option> | |
| 364 </param> | |
| 365 ## (-M) | |
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366 <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" /> |
| 0 | 367 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files |
| 368 ## (-o) | |
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369 <param name="outgroup_name" type="text" value="" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" /> |
| 0 | 370 ## (-O) |
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371 <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." /> |
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372 <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" /> |
| 0 | 373 ## (-q) |
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374 <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." /> |
| 0 | 375 ## (-r) |
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376 <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." /> |
| 0 | 377 ## (-R) |
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378 <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." /> |
| 0 | 379 ## (-s) source file option is in the required options section |
| 380 ## (-S) | |
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381 <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 '()<>[]{}' to define stem regions and pseudoknots."/> |
| 0 | 382 ## (-t) |
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383 <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." /> |
| 0 | 384 ## (-T) is hard-coded in the required options section |
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385 <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" /> |
| 0 | 386 ## (-U) |
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387 <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" /> |
| 0 | 388 ## (-V) |
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389 <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" /> |
| 0 | 390 ## (-W) |
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391 <param name="sliding_window_size" type="integer" 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'" /> |
| 0 | 392 ## (-x) - see it by the (-b) |
| 393 ## (-y) | |
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394 <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." /> |
| 0 | 395 ## (-z) |
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396 <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" /> |
| 0 | 397 </when> ## full option list |
| 398 </conditional> ## END $selExtraOpts | |
| 399 </inputs> | |
| 400 <outputs> | |
| 401 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" /> | |
| 402 ## REQUIRED | |
| 403 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log"> | |
| 404 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> | |
| 405 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 406 </data> | |
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407 <data format="nhx" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> |
| 0 | 408 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> |
| 409 </data> | |
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410 <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> |
| 0 | 411 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> |
| 412 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 413 </data> | |
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414 <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result"> |
| 0 | 415 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> |
| 416 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 417 </data> | |
| 418 ## ADVANCED | |
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419 <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree"> |
| 0 | 420 <filter>selExtraOpts['search_complete_random_tree'] is True</filter> |
| 421 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 422 </data> | |
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423 <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> |
| 0 | 424 <filter>(selExtraOpts['extraOptions'] == 'full')</filter> |
| 425 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '' or selExtraOpts['bootseed'] == '') and (selExtraOpts['search_algorithm'] == 'a')</filter> | |
| 426 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> | |
| 427 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter> | |
| 428 </data> | |
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429 <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> |
| 0 | 430 <filter>(selExtraOpts['extraOptions'] == "full")</filter> |
| 431 <filter>(selExtraOpts['multiple_model'] != '')</filter> | |
| 432 </data> | |
| 433 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions"> | |
| 434 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 435 <filter>selExtraOpts['multiple_model'] is not None </filter> | |
| 436 </data> | |
| 437 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log"> | |
| 438 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 439 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 440 <filter>(selExtraOpts['bootseed'] == '')</filter> | |
| 441 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> | |
| 442 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> | |
| 443 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 444 </data> | |
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445 <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result"> |
| 0 | 446 <filter>(selExtraOpts['extraOptions'] == "full")</filter> |
| 447 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 448 <filter>selExtraOpts['bootseed'] == ''</filter> | |
| 449 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 450 <filter>selExtraOpts['search_algorithm'] != 'b'</filter> | |
| 451 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 452 </data> | |
| 453 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions"> | |
| 454 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 455 <filter>(selExtraOpts['multiple_model'] is not None)</filter> | |
| 456 </data> | |
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457 <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> |
| 0 | 458 <filter>(selExtraOpts['extraOptions'] == "full")</filter> |
| 459 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 460 <filter>(selExtraOpts['bootseed'] == '')</filter> | |
| 461 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> | |
| 462 <filter>(selExtraOpts['constraint_file'] is None)</filter> | |
| 463 <filter>(selExtraOpts['groupingfile'] is None)</filter> | |
| 464 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter> | |
| 465 <filter>(selExtraOpts['start_tree_file'] is None)</filter> | |
| 466 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 467 </data> | |
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468 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees"> |
| 0 | 469 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 470 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter> | |
| 471 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter> | |
| 472 </data> | |
| 473 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions"> | |
| 474 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> | |
| 475 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 476 </data> | |
| 477 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels"> | |
| 478 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 479 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> | |
| 480 </data> | |
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481 <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree"> |
| 0 | 482 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 483 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter> | |
| 484 </data> | |
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485 <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree"> |
| 0 | 486 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 487 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter> | |
| 488 </data> | |
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489 <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree"> |
| 0 | 490 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 491 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter> | |
| 492 </data> | |
| 493 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences."> | |
| 494 <filter>selExtraOpts['search_algorithm'] == 'm' </filter> | |
| 495 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 496 </data> | |
| 497 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores"> | |
| 498 <filter>selExtraOpts['search_algorithm'] == 'g' </filter> | |
| 499 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 500 </data> | |
| 501 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances"> | |
| 502 <filter>selExtraOpts['search_algorithm'] == 'x' </filter> | |
| 503 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 504 </data> | |
| 505 </outputs> | |
| 506 <tests> | |
| 507 <test> | |
| 508 <param name="extraOptions" value="required"/> | |
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509 <param name="infile" value="dna.phy"/> |
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510 <param name="model_type" value="nucleotide"/> |
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511 <param name="base_model" value="GTRCAT"/> |
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512 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy"> |
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513 <output name="bestTreeReq"/> |
| 0 | 514 <assert_contents> |
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515 <has_text_matching expression="Frog" /> |
| 0 | 516 </assert_contents> |
| 517 </output> | |
| 518 </test> | |
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519 <test> |
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520 <param name="extraOptions" value="full"/> |
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521 <param name="infile" value="dna.fasta"/> |
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522 <param name="model_type" value="nucleotide"/> |
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523 <param name="base_model" value="GTRCAT"/> |
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524 <param name="number_of_runs" value="5"/> |
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525 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy"> |
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526 <output name="bestTreeReq"/> |
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527 <assert_contents> |
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528 <has_text_matching expression="Frog" /> |
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529 </assert_contents> |
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530 </output> |
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531 </test> |
| 0 | 532 </tests> |
| 533 <help> | |
| 534 Title: | |
| 535 ______ | |
| 536 Randomized Axelerated Maximum Likelihood | |
| 537 | |
| 538 Description: | |
| 539 ____________ | |
| 540 | |
| 541 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic | |
| 542 trees. The program is explicitly being developed to efficiently infer trees for | |
| 543 extremely large datasets, either in terms of the number of taxa and/or the | |
| 544 sequence length. | |
| 545 | |
| 546 URL: | |
| 547 ____ | |
| 548 Author's page: http://www.exelixis-lab.org/ | |
| 549 | |
| 550 Help: http://groups.google.com/group/raxml | |
| 551 | |
| 552 | |
| 553 Tool development: | |
| 554 ----------------- | |
| 555 Oleksandr Moskalenko with adaptations from Tiago Antao. | |
| 556 | |
| 557 </help> | |
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558 <citations> |
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559 <citation type="doi">10.1093/bioinformatics/btu033</citation> |
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560 <citation type="bibtex"> |
| 0 | 561 @article{stamatakis2014raxml, |
| 562 title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies}, | |
| 563 author={Stamatakis, Alexandros}, | |
| 564 journal={Bioinformatics}, | |
| 565 volume={30}, | |
| 566 number={9}, | |
| 567 pages={1312--1313}, | |
| 568 year={2014}, | |
| 569 publisher={Oxford Univ Press}} | |
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570 </citation> |
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571 </citations> |
| 0 | 572 </tool> |