Mercurial > repos > tiagoantao > raxml
annotate raxml.xml @ 37:04b7bf370a7a draft
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| author | tiagoantao |
|---|---|
| date | Fri, 13 Nov 2015 12:19:19 -0500 |
| parents | ec084125e45d |
| children | 2d72690325cf |
| 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 | |
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8 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 |
| 0 | 9 ## (-T) |
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10 ## Cannot have --threads 1 |
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11 #if $getVar("GALAXY_SLOTS", "1") == "1": |
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12 --binary "raxmlHPC" |
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13 else: |
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14 --binary "raxmlHPC-PTHREADS" |
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15 --threads \${GALAXY_SLOTS:-5} |
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16 #end if |
| 0 | 17 ## (-s) |
| 18 --source $infile | |
| 19 ## (-m) | |
| 20 --model_type $search_model_selector.model_type | |
| 21 --base_model $search_model_selector.base_model | |
| 22 #if str( $search_model_selector.model_type ) == 'aminoacid': | |
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23 $search_model_selector.aa_model_empirical_base_frequencies |
| 0 | 24 #if $search_model_selector.aa_search_matrix: |
| 25 --aa_search_matrix $search_model_selector.aa_search_matrix | |
| 26 #end if | |
| 27 #end if | |
| 28 ## (-p) | |
| 29 #if $random_seed: | |
| 30 --random_seed $random_seed | |
| 31 #else | |
| 32 --random_seed 1234567890 | |
| 33 #end if | |
| 34 | |
| 35 ## Optional parameters | |
| 36 | |
| 37 #if str( $selExtraOpts.extraOptions ) == 'full': | |
| 38 ## (-N/#) | |
| 39 #if $selExtraOpts.number_of_runs: | |
| 40 --number_of_runs $selExtraOpts.number_of_runs | |
| 41 #end if | |
| 42 #if $selExtraOpts.number_of_runs_bootstop: | |
| 43 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop | |
| 44 #end if | |
| 45 ## (-a) | |
| 46 #if $selExtraOpts.weightfile: | |
| 47 --weightfile $selExtraOpts.weightfile | |
| 48 #end if | |
| 49 ## (-b) | |
| 50 #if str ($selExtraOpts.secondary_structure_model) != "": | |
| 51 --secondary_structure_model $selExtraOpts.secondary_structure_model | |
| 52 #end if | |
| 53 ## (-b) | |
| 54 #if $selExtraOpts.bootseed: | |
| 55 --bootseed $selExtraOpts.bootseed | |
| 56 #end if | |
| 57 ## (-c) | |
| 58 #if $selExtraOpts.numofcats: | |
| 59 --numofcats $selExtraOpts.numofcats | |
| 60 #end if | |
| 61 ## (-d) | |
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62 $selExtraOpts.search_complete_random_tree |
| 0 | 63 ## (-D) |
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64 $selExtraOpts.ml_search_convergence |
| 0 | 65 ## (-e) |
| 66 #if $selExtraOpts.model_opt_precision: | |
| 67 --model_opt_precision $selExtraOpts.model_opt_precision | |
| 68 #end if | |
| 69 ## (-E) | |
| 70 #if $selExtraOpts.excludefile: | |
| 71 --excludefile $selExtraOpts.excludefile | |
| 72 #end if | |
| 73 ## (-f) | |
| 74 #if $selExtraOpts.search_algorithm: | |
| 75 --search_algorithm $selExtraOpts.search_algorithm | |
| 76 #end if | |
| 77 ## (-F) | |
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78 $selExtraOpts.save_memory_cat_model |
| 0 | 79 ## (-g) |
| 80 #if $selExtraOpts.groupingfile: | |
| 81 --groupingfile $selExtraOpts.groupingfile | |
| 82 #end if | |
| 83 ## (-G) | |
| 84 #if $selExtraOpts.enable_evol_heuristics: | |
| 85 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics | |
| 86 #end if | |
| 87 ## (-i) | |
| 88 #if $selExtraOpts.initial_rearrangement_setting: | |
| 89 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting | |
| 90 #end if | |
| 91 ## (-I) | |
| 92 #if $selExtraOpts.posterior_bootstopping_analysis: | |
| 93 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis | |
| 94 #end if | |
| 95 ## (-J) | |
| 96 #if $selExtraOpts.majority_rule_consensus: | |
| 97 --majority_rule_consensus $selExtraOpts.majority_rule_consensus | |
| 98 #end if | |
| 99 ## (-k) | |
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100 $selExtraOpts.print_branch_lengths |
| 0 | 101 ## (-K) |
| 102 #if str ($selExtraOpts.multistate_sub_model) != "": | |
| 103 --multistate_sub_model $selExtraOpts.multistate_sub_model | |
| 104 #end if | |
| 105 ## (-m) - see elsewhere | |
| 106 ## (-M) | |
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107 $selExtraOpts.estimate_individual_branch_lengths |
| 0 | 108 ## (-n) - see elsewhere |
| 109 ## (-o) | |
| 110 #if $selExtraOpts.outgroup_name: | |
| 111 --outgroup_name $selExtraOpts.outgroup_name | |
| 112 #end if | |
| 113 ## (-O) | |
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114 $selExtraOpts.disable_undetermined_seq_check |
| 0 | 115 ## (-P) |
| 116 #if $selExtraOpts.external_protein_model: | |
| 117 --external_protein_model $selExtraOpts.external_protein_model | |
| 118 #end if | |
| 119 ## (-q) | |
| 120 #if $selExtraOpts.multiple_model: | |
| 121 --multiple_model $selExtraOpts.multiple_model | |
| 122 #end if | |
| 123 ## (-r) | |
| 124 #if $selExtraOpts.constraint_file: | |
| 125 --constraint_file $selExtraOpts.constraint_file | |
| 126 #end if | |
| 127 ## (-R) | |
| 128 #if $selExtraOpts.bin_model_parameter_file: | |
| 129 --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file | |
| 130 #end if | |
| 131 ## (-S) | |
| 132 #if $selExtraOpts.secondary_structure_file: | |
| 133 --secondary_structure_file $selExtraOpts.secondary_structure_file | |
| 134 #end if | |
| 135 ## (-t) | |
| 136 #if $selExtraOpts.start_tree_file: | |
| 137 --starting_tree $selExtraOpts.start_tree_file | |
| 138 #end if | |
| 139 ## (-T) see elsewhere | |
| 140 ## (-u) | |
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141 $selExtraOpts.use_median_approximation |
| 0 | 142 ## (-U) |
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143 $selExtraOpts.save_memory_gappy_alignments |
| 0 | 144 ## (-V) |
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145 $selExtraOpts.disable_rate_heterogeneity |
| 0 | 146 ## (-W) |
| 147 #if $selExtraOpts.sliding_window_size: | |
| 148 --sliding_window_size $selExtraOpts.sliding_window_size | |
| 149 #end if | |
| 150 ## (-x) | |
| 151 #if $selExtraOpts.rapid_bootstrap_random_seed: | |
| 152 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed | |
| 153 #end if | |
| 154 ## (-y) | |
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155 $selExtraOpts.parsimony_starting_tree_only |
| 0 | 156 ## (-z) |
| 157 #if $selExtraOpts.file_multiple_trees: | |
| 158 --file_multiple_trees $selExtraOpts.file_multiple_trees | |
| 159 #end if | |
| 160 #end if | |
| 161 | |
| 162 </command> | |
| 163 <inputs> | |
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164 ## (-s) |
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165 <param type="data" format="fasta,phylip" name="infile" label="Source file"/> |
| 0 | 166 ## (-m) |
| 167 <conditional name="search_model_selector"> | |
| 168 <param name="model_type" type="select" label="Model Type"> | |
| 169 <option value="nucleotide" selected="true">Nucleotide</option> | |
| 170 <option value="aminoacid">Amino Acid</option> | |
| 171 <option value="binary">Binary</option> | |
| 172 <option value="multistate">Multistate</option> | |
| 173 </param> | |
| 174 <when value="nucleotide"> | |
| 175 ## Nucleotide substitution models | |
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176 <param name="base_model" type="select" label="Substitution Model"> |
| 0 | 177 <option value="GTRCAT">GTRCAT</option> |
| 178 <option value="GTRCATI">GTRCATI</option> | |
| 179 <option value="GTRGAMMA" select="true">GTRGAMMA</option> | |
| 180 <option value="GTRGAMMAI">GTRGAMMAI</option> | |
| 181 </param> | |
| 182 </when> | |
| 183 ## Aminoacid substitution models | |
| 184 <when value="aminoacid"> | |
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185 <param name="aa_model_empirical_base_frequencies" |
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186 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" /> |
| 0 | 187 <param name="base_model" type="select" label="Substitution Model (-m)"> |
| 188 <option value="PROTCAT" select="true">PROTCAT</option> | |
| 189 <option value="PROTCATI">PROTCATI</option> | |
| 190 <option value="PROTGAMMA">PROTGAMMA</option> | |
| 191 <option value="PROTGAMMAI">PROTGAMMAI</option> | |
| 192 </param> | |
| 193 <param name="aa_search_matrix" type="select" label="Matrix"> | |
| 194 <option value="DAYHOFF" select="true">DAYHOFF</option> | |
| 195 <option value="DCMUT">DCMUT</option> | |
| 196 <option value="JTT">JTT</option> | |
| 197 <option value="MTREV">MTREV</option> | |
| 198 <option value="WAG">WAG</option> | |
| 199 <option value="RTREV">RTREV</option> | |
| 200 <option value="CPREV">CPREV</option> | |
| 201 <option value="VT">VT</option> | |
| 202 <option value="BLOSUM62">BLOSUM62</option> | |
| 203 <option value="MTMAM">MTMAM</option> | |
| 204 <option value="LG">LG</option> | |
| 205 <option value="MTART">MTART</option> | |
| 206 <option value="MTZOA">MTZOA</option> | |
| 207 <option value="PMB">PMB</option> | |
| 208 <option value="HIVB">HIVB</option> | |
| 209 <option value="HIVW">HIVW</option> | |
| 210 <option value="JTTDCMUT">JTTDCMUT</option> | |
| 211 <option value="FLU">FLU</option> | |
| 212 <option value="DUMMY">DUMMY</option> | |
| 213 <option value="DUMMY2">DUMMY2</option> | |
| 214 <option value="GTR_UNLINKED">GTR_UNLINKED</option> | |
| 215 <option value="GTR">GTR</option> | |
| 216 </param> | |
| 217 </when> | |
| 218 ## Binary substitution models | |
| 219 <when value="binary"> | |
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220 <param name="base_model" type="select" label="Substitution Model"> |
| 0 | 221 <option value="BINCAT">BINCAT</option> |
| 222 <option value="BINCATI">BINCATI</option> | |
| 223 <option value="BINGAMMA">BINGAMMA</option> | |
| 224 <option value="BINGAMMAI">BINGAMMAI</option> | |
| 225 </param> | |
| 226 </when> | |
| 227 ## Multi-state substitution models | |
| 228 <when value="multistate"> | |
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229 <param name="base_model" type="select" label="Substitution Model"> |
| 0 | 230 <option value="MULTICAT">MULTICAT</option> |
| 231 <option value="MULTICATI">MULTICATI</option> | |
| 232 <option value="MULTIGAMMA">MULTIGAMMA</option> | |
| 233 <option value="MULTIGAMMAI">MULTIGAMMAI</option> | |
| 234 </param> | |
| 235 </when> | |
| 236 </conditional> | |
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237 <param name="random_seed" type="integer" value="1234567890" label="Random |
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238 seed used for the parsimony inferences" /> |
| 0 | 239 <conditional name="selExtraOpts"> |
| 240 <param name="extraOptions" type="select" label="RAxML options to use" | |
| 241 help="The required minimal settings are the input file and the | |
| 242 substitution model. To specify extra options select the 'Full option list'"> | |
| 243 <option value="required">Required options only</option> | |
| 244 <option value="full">Full option list</option> | |
| 245 </param> | |
| 246 <when value="full"> | |
| 247 ## (-N/#) | |
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248 <param name="number_of_runs" type="integer" value="" |
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249 label="Number of runs" help="Specify the number of |
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250 alternative runs (-N|#) on distinct starting trees In combination |
| 0 | 251 with the '-b' option will invoke a multiple boostrap analysis. |
| 252 You can add the bootstopping criteria by choosing the autoMR, | |
| 253 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of | |
| 254 providing a number here. Bootstopping will only work in | |
| 255 combination with '-x' or '-b'." | |
| 256 optional="True" /> | |
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257 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True"> |
| 0 | 258 <option value="" selected="yes"></option> |
| 259 <option value="autoMR">autoMR</option> | |
| 260 <option value="autoMRE">autoMRE</option> | |
| 261 <option value="autoMRE_IGN">autoMRE_IGN</option> | |
| 262 <option value="autoFC">autoFC</option> | |
| 263 </param> | |
| 264 ## Alphabetical Listing of Advanced Options | |
| 265 ## (-a) | |
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266 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" /> |
| 0 | 267 ## (-A) |
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268 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True"> |
| 0 | 269 <option value="" selected="yes"></option> |
| 270 <option value="S6A">S6A</option> | |
| 271 <option value="S6B">S6B</option> | |
| 272 <option value="S6C">S6C</option> | |
| 273 <option value="S6D">S6D</option> | |
| 274 <option value="S6E">S6E</option> | |
| 275 <option value="S7A">S7A</option> | |
| 276 <option value="S7B">S7B</option> | |
| 277 <option value="S7C">S7C</option> | |
| 278 <option value="S7D">S7D</option> | |
| 279 <option value="S7E">S7E</option> | |
| 280 <option value="S7F">S7F</option> | |
| 281 <option value="S16">S16</option> | |
| 282 <option value="S16A">S16A</option> | |
| 283 <option value="S16B">S16B</option> | |
| 284 </param> | |
| 285 ## (-b) | |
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286 <param name="bootseed" type="integer" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true' optional="True" /> |
| 0 | 287 ## (-x) |
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288 <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 | 289 ## (-B) |
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290 <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 | 291 ## (-c) |
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292 <param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" /> |
| 0 | 293 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. |
| 294 ## (-d) | |
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295 <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 | 296 ## (-D) |
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297 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" /> |
| 0 | 298 ## (-e) |
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299 <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 | 300 ## (-E) |
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301 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" /> |
| 0 | 302 ## (-f) |
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303 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True"> |
| 0 | 304 <option value="a">Rapid bootstrap and best ML tree search (a)</option> |
| 305 <option value="A">Compute marginal ancestral states (A)</option> | |
| 306 <option value="b">Draw bipartition information (b)</option> | |
| 307 <option value="c">Check if the alignment can be read (c)</option> | |
| 308 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option> | |
| 309 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option> | |
| 310 <option value="g">Compute per-site log likelihoods for -z trees (g)</option> | |
| 311 <option value="h">Compute log likelihood test for -t / -z trees (h)</option> | |
| 312 <option value="j">Generate bootstrapped alignment files (j)</option> | |
| 313 <option value="J">Compute SH-like support values for the -t tree (J)</option> | |
| 314 <option value="m">Compare bipartitions between -t and -z trees (m)</option> | |
| 315 <option value="n">Compute log likelihood score for -z trees (n)</option> | |
| 316 <option value="o">Use old slower search algorithm (o)</option> | |
| 317 <option value="p">Stepwise MP addition of new sequences (p)</option> | |
| 318 <option value="q">Fast quartet calculator (q)</option> | |
| 319 <option value="r">Compute pairwise RF distances in -z trees (r)</option> | |
| 320 <option value="s">Split a multi-gene alignment (s)</option> | |
| 321 <option value="S">Compute site-specific placement bias (S)</option> | |
| 322 <option value="t">Randomized tree searches on a fixed starting tree (t)</option> | |
| 323 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option> | |
| 324 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option> | |
| 325 <option value="v">Classify environmental sequences (v)</option> | |
| 326 <option value="w">Compute ELW-test on -z trees (w)</option> | |
| 327 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option> | |
| 328 <option value="y">Classify environmental sequences into a reference tree (y)</option> | |
| 329 </param> | |
| 330 ## (-F) | |
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331 <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 | 332 ## (-g) |
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333 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" /> |
| 0 | 334 ## (-G) |
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335 <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 | 336 <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/> |
| 337 </param> | |
| 338 ## (-i) | |
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339 <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" /> |
| 0 | 340 ## (-I) |
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341 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True"> |
| 0 | 342 <option value="" selected="True"></option> |
| 343 <option value="autoFC">Frequency-based criterion (autoFC)</option> | |
| 344 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option> | |
| 345 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option> | |
| 346 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option> | |
| 347 </param> | |
| 348 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy | |
| 349 ## (-J) | |
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350 <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True"> |
| 0 | 351 <option value="" selected="True"></option> |
| 352 <option value="MR">Majority-rule consensus tree (MR)</option> | |
| 353 <option value="MRE">Extended majority-rule consensus tree (MRE)</option> | |
| 354 <option value="STRICT">Strict consensus tree (STRICT)</option> | |
| 355 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option> | |
| 356 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option> | |
| 357 </param> | |
| 358 ## (-k) | |
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359 <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 | 360 ## (-K) |
| 361 <param name="multistate_sub_model" type="select" label="Specify a | |
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362 multi-state substitution model" optional="True"> |
| 0 | 363 <option value="" selected="true"></option> |
| 364 <option value="GTR">GTR</option> | |
| 365 <option value="ORDERED">ORDERED</option> | |
| 366 <option value="MK">MK</option> | |
| 367 </param> | |
| 368 ## (-M) | |
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369 <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 | 370 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files |
| 371 ## (-o) | |
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372 <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 | 373 ## (-O) |
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374 <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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375 <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 | 376 ## (-q) |
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377 <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 | 378 ## (-r) |
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379 <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 | 380 ## (-R) |
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381 <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 | 382 ## (-s) source file option is in the required options section |
| 383 ## (-S) | |
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384 <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 | 385 ## (-t) |
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386 <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 | 387 ## (-T) is hard-coded in the required options section |
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388 <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 | 389 ## (-U) |
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390 <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 | 391 ## (-V) |
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392 <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 | 393 ## (-W) |
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394 <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 | 395 ## (-x) - see it by the (-b) |
| 396 ## (-y) | |
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397 <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 | 398 ## (-z) |
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399 <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 | 400 </when> ## full option list |
| 401 </conditional> ## END $selExtraOpts | |
| 402 </inputs> | |
| 403 <outputs> | |
| 404 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" /> | |
| 405 ## REQUIRED | |
| 406 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log"> | |
| 407 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> | |
| 408 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 409 </data> | |
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410 <data format="nhx" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> |
| 0 | 411 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> |
| 412 </data> | |
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413 <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> |
| 0 | 414 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> |
| 415 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 416 </data> | |
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417 <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result"> |
| 0 | 418 <filter>(selExtraOpts['extraOptions'] == 'required')</filter> |
| 419 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 420 </data> | |
| 421 ## ADVANCED | |
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422 <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree"> |
| 0 | 423 <filter>selExtraOpts['search_complete_random_tree'] is True</filter> |
| 424 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 425 </data> | |
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426 <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> |
| 0 | 427 <filter>(selExtraOpts['extraOptions'] == 'full')</filter> |
| 428 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> | |
| 429 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter> | |
| 430 </data> | |
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431 <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> |
| 0 | 432 <filter>(selExtraOpts['extraOptions'] == "full")</filter> |
| 433 <filter>(selExtraOpts['multiple_model'] != '')</filter> | |
| 434 </data> | |
| 435 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions"> | |
| 436 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 437 <filter>selExtraOpts['multiple_model'] is not None </filter> | |
| 438 </data> | |
| 439 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log"> | |
| 440 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 441 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 442 <filter>(selExtraOpts['bootseed'] == '')</filter> | |
| 443 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> | |
| 444 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter> | |
| 445 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 446 </data> | |
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447 <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result"> |
| 0 | 448 <filter>(selExtraOpts['extraOptions'] == "full")</filter> |
| 449 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 450 <filter>selExtraOpts['bootseed'] == ''</filter> | |
| 451 <filter>selExtraOpts['search_algorithm'] != 'a'</filter> | |
| 452 <filter>selExtraOpts['search_algorithm'] != 'b'</filter> | |
| 453 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 454 </data> | |
| 455 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions"> | |
| 456 <filter>(selExtraOpts['extraOptions'] == "full")</filter> | |
| 457 <filter>(selExtraOpts['multiple_model'] is not None)</filter> | |
| 458 </data> | |
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459 <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> |
| 0 | 460 <filter>(selExtraOpts['extraOptions'] == "full")</filter> |
| 461 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter> | |
| 462 <filter>(selExtraOpts['bootseed'] == '')</filter> | |
| 463 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter> | |
| 464 <filter>(selExtraOpts['constraint_file'] is None)</filter> | |
| 465 <filter>(selExtraOpts['groupingfile'] is None)</filter> | |
| 466 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter> | |
| 467 <filter>(selExtraOpts['start_tree_file'] is None)</filter> | |
| 468 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter> | |
| 469 </data> | |
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470 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees"> |
| 0 | 471 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 472 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter> | |
| 473 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter> | |
| 474 </data> | |
| 475 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions"> | |
| 476 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> | |
| 477 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 478 </data> | |
| 479 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels"> | |
| 480 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 481 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter> | |
| 482 </data> | |
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483 <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree"> |
| 0 | 484 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 485 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter> | |
| 486 </data> | |
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487 <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree"> |
| 0 | 488 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 489 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter> | |
| 490 </data> | |
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491 <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree"> |
| 0 | 492 <filter>selExtraOpts['extraOptions'] == "full"</filter> |
| 493 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter> | |
| 494 </data> | |
| 495 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences."> | |
| 496 <filter>selExtraOpts['search_algorithm'] == 'm' </filter> | |
| 497 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 498 </data> | |
| 499 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores"> | |
| 500 <filter>selExtraOpts['search_algorithm'] == 'g' </filter> | |
| 501 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 502 </data> | |
| 503 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances"> | |
| 504 <filter>selExtraOpts['search_algorithm'] == 'x' </filter> | |
| 505 <filter>selExtraOpts['extraOptions'] == "full"</filter> | |
| 506 </data> | |
| 507 </outputs> | |
| 508 <tests> | |
| 509 <test> | |
| 510 <param name="extraOptions" value="required"/> | |
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511 <param name="infile" value="dna.phy"/> |
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512 <param name="model_type" value="nucleotide"/> |
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513 <param name="base_model" value="GTRCAT"/> |
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514 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy"> |
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515 <output name="bestTreeReq"/> |
| 0 | 516 <assert_contents> |
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517 <has_text_matching expression="Frog" /> |
| 0 | 518 </assert_contents> |
| 519 </output> | |
| 520 </test> | |
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521 <test> |
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522 <param name="extraOptions" value="full"/> |
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523 <param name="infile" value="dna.fasta"/> |
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524 <param name="model_type" value="nucleotide"/> |
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525 <param name="base_model" value="GTRCAT"/> |
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526 <param name="number_of_runs" value="5"/> |
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527 <output name="parsimonyTree" file="RAxML_parsimonyTree.galaxy"> |
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528 <output name="bestTree"/> |
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529 <assert_contents> |
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531 </assert_contents> |
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532 </output> |
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533 </test> |
| 0 | 534 </tests> |
| 535 <help> | |
| 536 Title: | |
| 537 ______ | |
| 538 Randomized Axelerated Maximum Likelihood | |
| 539 | |
| 540 Description: | |
| 541 ____________ | |
| 542 | |
| 543 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic | |
| 544 trees. The program is explicitly being developed to efficiently infer trees for | |
| 545 extremely large datasets, either in terms of the number of taxa and/or the | |
| 546 sequence length. | |
| 547 | |
| 548 URL: | |
| 549 ____ | |
| 550 Author's page: http://www.exelixis-lab.org/ | |
| 551 | |
| 552 Help: http://groups.google.com/group/raxml | |
| 553 | |
| 554 | |
| 555 Tool development: | |
| 556 ----------------- | |
| 557 Oleksandr Moskalenko with adaptations from Tiago Antao. | |
| 558 | |
| 559 </help> | |
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560 <citations> |
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561 <citation type="doi">10.1093/bioinformatics/btu033</citation> |
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562 <citation type="bibtex"> |
| 0 | 563 @article{stamatakis2014raxml, |
| 564 title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies}, | |
| 565 author={Stamatakis, Alexandros}, | |
| 566 journal={Bioinformatics}, | |
| 567 volume={30}, | |
| 568 number={9}, | |
| 569 pages={1312--1313}, | |
| 570 year={2014}, | |
| 571 publisher={Oxford Univ Press}} | |
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572 </citation> |
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573 </citations> |
| 0 | 574 </tool> |