Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_phylogeny_iqtree.xml @ 20:d93d8888f0b0 draft
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| author | florianbegusch |
|---|---|
| date | Fri, 04 Sep 2020 12:44:24 +0000 |
| parents | |
| children |
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| 19:6c48f8d82424 | 20:d93d8888f0b0 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree" | |
| 3 version="2020.8"> | |
| 4 <description>Construct a phylogenetic tree with IQ-TREE.</description> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="2020.8">qiime2</requirement> | |
| 7 </requirements> | |
| 8 <command><![CDATA[ | |
| 9 qiime phylogeny iqtree | |
| 10 | |
| 11 --i-alignment=$ialignment | |
| 12 | |
| 13 #if str($pseed): | |
| 14 --p-seed=$pseed | |
| 15 #end if | |
| 16 #if str($pncores) != 'None': | |
| 17 --p-n-cores=$pncores | |
| 18 #end if | |
| 19 | |
| 20 #set $pncoresmax = '${GALAXY_SLOTS:-4}' | |
| 21 | |
| 22 #if str($pncoresmax): | |
| 23 --p-n-cores-max=$pncoresmax | |
| 24 #end if | |
| 25 | |
| 26 --p-n-runs=$pnruns | |
| 27 | |
| 28 #if str($psubstitutionmodel) != 'None': | |
| 29 --p-substitution-model=$psubstitutionmodel | |
| 30 #end if | |
| 31 | |
| 32 #if str($pninitparstrees): | |
| 33 --p-n-init-pars-trees=$pninitparstrees | |
| 34 #end if | |
| 35 #if str($pntopinittrees): | |
| 36 --p-n-top-init-trees=$pntopinittrees | |
| 37 #end if | |
| 38 #if str($pnbestretaintrees): | |
| 39 --p-n-best-retain-trees=$pnbestretaintrees | |
| 40 #end if | |
| 41 #if str($pniter): | |
| 42 --p-n-iter=$pniter | |
| 43 #end if | |
| 44 #if str($pstopiter): | |
| 45 --p-stop-iter=$pstopiter | |
| 46 #end if | |
| 47 #if str($pperturbnnistrength): | |
| 48 --p-perturb-nni-strength=$pperturbnnistrength | |
| 49 #end if | |
| 50 #if str($psprradius): | |
| 51 --p-spr-radius=$psprradius | |
| 52 #end if | |
| 53 #if $pallnni: | |
| 54 --p-allnni | |
| 55 #end if | |
| 56 | |
| 57 #if $pfast: | |
| 58 --p-fast | |
| 59 #end if | |
| 60 | |
| 61 #if str($palrt): | |
| 62 --p-alrt=$palrt | |
| 63 #end if | |
| 64 #if $pabayes: | |
| 65 --p-abayes | |
| 66 #end if | |
| 67 | |
| 68 #if str($plbp): | |
| 69 --p-lbp=$plbp | |
| 70 #end if | |
| 71 #if $psafe: | |
| 72 --p-safe | |
| 73 #end if | |
| 74 | |
| 75 --o-tree=otree | |
| 76 | |
| 77 #if str($examples) != 'None': | |
| 78 --examples=$examples | |
| 79 #end if | |
| 80 | |
| 81 ; | |
| 82 cp otree.qza $otree | |
| 83 | |
| 84 ]]></command> | |
| 85 <inputs> | |
| 86 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" /> | |
| 87 <param label="--p-seed: INTEGER Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="False" type="text" /> | |
| 88 <param label="--p-n-cores: " name="pncores" optional="True" type="select"> | |
| 89 <option selected="True" value="None">Selection is Optional</option> | |
| 90 <option value="Int % Range(1">Int % Range(1</option> | |
| 91 <option value="None">None</option> | |
| 92 </param> | |
| 93 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" min="1" name="pnruns" optional="True" type="integer" value="1" /> | |
| 94 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select"> | |
| 95 <option selected="True" value="None">Selection is Optional</option> | |
| 96 <option value="JC">JC</option> | |
| 97 <option value="JC+I">JC+I</option> | |
| 98 <option value="JC+G">JC+G</option> | |
| 99 <option value="JC+I+G">JC+I+G</option> | |
| 100 <option value="JC+R2">JC+R2</option> | |
| 101 <option value="JC+R3">JC+R3</option> | |
| 102 <option value="JC+R4">JC+R4</option> | |
| 103 <option value="JC+R5">JC+R5</option> | |
| 104 <option value="JC+R6">JC+R6</option> | |
| 105 <option value="JC+R7">JC+R7</option> | |
| 106 <option value="JC+R8">JC+R8</option> | |
| 107 <option value="JC+R9">JC+R9</option> | |
| 108 <option value="JC+R10">JC+R10</option> | |
| 109 <option value="F81">F81</option> | |
| 110 <option value="F81+I">F81+I</option> | |
| 111 <option value="F81+G">F81+G</option> | |
| 112 <option value="F81+I+G">F81+I+G</option> | |
| 113 <option value="F81+R2">F81+R2</option> | |
| 114 <option value="F81+R3">F81+R3</option> | |
| 115 <option value="F81+R4">F81+R4</option> | |
| 116 <option value="F81+R5">F81+R5</option> | |
| 117 <option value="F81+R6">F81+R6</option> | |
| 118 <option value="F81+R7">F81+R7</option> | |
| 119 <option value="F81+R8">F81+R8</option> | |
| 120 <option value="F81+R9">F81+R9</option> | |
| 121 <option value="F81+R10">F81+R10</option> | |
| 122 <option value="K80">K80</option> | |
| 123 <option value="K80+I">K80+I</option> | |
| 124 <option value="K80+G">K80+G</option> | |
| 125 <option value="K80+I+G">K80+I+G</option> | |
| 126 <option value="K80+R2">K80+R2</option> | |
| 127 <option value="K80+R3">K80+R3</option> | |
| 128 <option value="K80+R4">K80+R4</option> | |
| 129 <option value="K80+R5">K80+R5</option> | |
| 130 <option value="K80+R6">K80+R6</option> | |
| 131 <option value="K80+R7">K80+R7</option> | |
| 132 <option value="K80+R8">K80+R8</option> | |
| 133 <option value="K80+R9">K80+R9</option> | |
| 134 <option value="K80+R10">K80+R10</option> | |
| 135 <option value="HKY">HKY</option> | |
| 136 <option value="HKY+I">HKY+I</option> | |
| 137 <option value="HKY+G">HKY+G</option> | |
| 138 <option value="HKY+I+G">HKY+I+G</option> | |
| 139 <option value="HKY+R2">HKY+R2</option> | |
| 140 <option value="HKY+R3">HKY+R3</option> | |
| 141 <option value="HKY+R4">HKY+R4</option> | |
| 142 <option value="HKY+R5">HKY+R5</option> | |
| 143 <option value="HKY+R6">HKY+R6</option> | |
| 144 <option value="HKY+R7">HKY+R7</option> | |
| 145 <option value="HKY+R8">HKY+R8</option> | |
| 146 <option value="HKY+R9">HKY+R9</option> | |
| 147 <option value="HKY+R10">HKY+R10</option> | |
| 148 <option value="TNe">TNe</option> | |
| 149 <option value="TNe+I">TNe+I</option> | |
| 150 <option value="TNe+G">TNe+G</option> | |
| 151 <option value="TNe+I+G">TNe+I+G</option> | |
| 152 <option value="TNe+R2">TNe+R2</option> | |
| 153 <option value="TNe+R3">TNe+R3</option> | |
| 154 <option value="TNe+R4">TNe+R4</option> | |
| 155 <option value="TNe+R5">TNe+R5</option> | |
| 156 <option value="TNe+R6">TNe+R6</option> | |
| 157 <option value="TNe+R7">TNe+R7</option> | |
| 158 <option value="TNe+R8">TNe+R8</option> | |
| 159 <option value="TNe+R9">TNe+R9</option> | |
| 160 <option value="TNe+R10">TNe+R10</option> | |
| 161 <option value="TN">TN</option> | |
| 162 <option value="TN+I">TN+I</option> | |
| 163 <option value="TN+G">TN+G</option> | |
| 164 <option value="TN+I+G">TN+I+G</option> | |
| 165 <option value="TN+R2">TN+R2</option> | |
| 166 <option value="TN+R3">TN+R3</option> | |
| 167 <option value="TN+R4">TN+R4</option> | |
| 168 <option value="TN+R5">TN+R5</option> | |
| 169 <option value="TN+R6">TN+R6</option> | |
| 170 <option value="TN+R7">TN+R7</option> | |
| 171 <option value="TN+R8">TN+R8</option> | |
| 172 <option value="TN+R9">TN+R9</option> | |
| 173 <option value="TN+R10">TN+R10</option> | |
| 174 <option value="K81">K81</option> | |
| 175 <option value="K81+I">K81+I</option> | |
| 176 <option value="K81+G">K81+G</option> | |
| 177 <option value="K81+I+G">K81+I+G</option> | |
| 178 <option value="K81+R2">K81+R2</option> | |
| 179 <option value="K81+R3">K81+R3</option> | |
| 180 <option value="K81+R4">K81+R4</option> | |
| 181 <option value="K81+R5">K81+R5</option> | |
| 182 <option value="K81+R6">K81+R6</option> | |
| 183 <option value="K81+R7">K81+R7</option> | |
| 184 <option value="K81+R8">K81+R8</option> | |
| 185 <option value="K81+R9">K81+R9</option> | |
| 186 <option value="K81+R10">K81+R10</option> | |
| 187 <option value="K81u">K81u</option> | |
| 188 <option value="K81u+I">K81u+I</option> | |
| 189 <option value="K81u+G">K81u+G</option> | |
| 190 <option value="K81u+I+G">K81u+I+G</option> | |
| 191 <option value="K81u+R2">K81u+R2</option> | |
| 192 <option value="K81u+R3">K81u+R3</option> | |
| 193 <option value="K81u+R4">K81u+R4</option> | |
| 194 <option value="K81u+R5">K81u+R5</option> | |
| 195 <option value="K81u+R6">K81u+R6</option> | |
| 196 <option value="K81u+R7">K81u+R7</option> | |
| 197 <option value="K81u+R8">K81u+R8</option> | |
| 198 <option value="K81u+R9">K81u+R9</option> | |
| 199 <option value="K81u+R10">K81u+R10</option> | |
| 200 <option value="TPM2">TPM2</option> | |
| 201 <option value="TPM2+I">TPM2+I</option> | |
| 202 <option value="TPM2+G">TPM2+G</option> | |
| 203 <option value="TPM2+I+G">TPM2+I+G</option> | |
| 204 <option value="TPM2+R2">TPM2+R2</option> | |
| 205 <option value="TPM2+R3">TPM2+R3</option> | |
| 206 <option value="TPM2+R4">TPM2+R4</option> | |
| 207 <option value="TPM2+R5">TPM2+R5</option> | |
| 208 <option value="TPM2+R6">TPM2+R6</option> | |
| 209 <option value="TPM2+R7">TPM2+R7</option> | |
| 210 <option value="TPM2+R8">TPM2+R8</option> | |
| 211 <option value="TPM2+R9">TPM2+R9</option> | |
| 212 <option value="TPM2+R10">TPM2+R10</option> | |
| 213 <option value="TPM2u">TPM2u</option> | |
| 214 <option value="TPM2u+I">TPM2u+I</option> | |
| 215 <option value="TPM2u+G">TPM2u+G</option> | |
| 216 <option value="TPM2u+I+G">TPM2u+I+G</option> | |
| 217 <option value="TPM2u+R2">TPM2u+R2</option> | |
| 218 <option value="TPM2u+R3">TPM2u+R3</option> | |
| 219 <option value="TPM2u+R4">TPM2u+R4</option> | |
| 220 <option value="TPM2u+R5">TPM2u+R5</option> | |
| 221 <option value="TPM2u+R6">TPM2u+R6</option> | |
| 222 <option value="TPM2u+R7">TPM2u+R7</option> | |
| 223 <option value="TPM2u+R8">TPM2u+R8</option> | |
| 224 <option value="TPM2u+R9">TPM2u+R9</option> | |
| 225 <option value="TPM2u+R10">TPM2u+R10</option> | |
| 226 <option value="TPM3">TPM3</option> | |
| 227 <option value="TPM3+I">TPM3+I</option> | |
| 228 <option value="TPM3+G">TPM3+G</option> | |
| 229 <option value="TPM3+I+G">TPM3+I+G</option> | |
| 230 <option value="TPM3+R2">TPM3+R2</option> | |
| 231 <option value="TPM3+R3">TPM3+R3</option> | |
| 232 <option value="TPM3+R4">TPM3+R4</option> | |
| 233 <option value="TPM3+R5">TPM3+R5</option> | |
| 234 <option value="TPM3+R6">TPM3+R6</option> | |
| 235 <option value="TPM3+R7">TPM3+R7</option> | |
| 236 <option value="TPM3+R8">TPM3+R8</option> | |
| 237 <option value="TPM3+R9">TPM3+R9</option> | |
| 238 <option value="TPM3+R10">TPM3+R10</option> | |
| 239 <option value="TPM3u">TPM3u</option> | |
| 240 <option value="TPM3u+I">TPM3u+I</option> | |
| 241 <option value="TPM3u+G">TPM3u+G</option> | |
| 242 <option value="TPM3u+I+G">TPM3u+I+G</option> | |
| 243 <option value="TPM3u+R2">TPM3u+R2</option> | |
| 244 <option value="TPM3u+R3">TPM3u+R3</option> | |
| 245 <option value="TPM3u+R4">TPM3u+R4</option> | |
| 246 <option value="TPM3u+R5">TPM3u+R5</option> | |
| 247 <option value="TPM3u+R6">TPM3u+R6</option> | |
| 248 <option value="TPM3u+R7">TPM3u+R7</option> | |
| 249 <option value="TPM3u+R8">TPM3u+R8</option> | |
| 250 <option value="TPM3u+R9">TPM3u+R9</option> | |
| 251 <option value="TPM3u+R10">TPM3u+R10</option> | |
| 252 <option value="TIMe">TIMe</option> | |
| 253 <option value="TIMe+I">TIMe+I</option> | |
| 254 <option value="TIMe+G">TIMe+G</option> | |
| 255 <option value="TIMe+I+G">TIMe+I+G</option> | |
| 256 <option value="TIMe+R2">TIMe+R2</option> | |
| 257 <option value="TIMe+R3">TIMe+R3</option> | |
| 258 <option value="TIMe+R4">TIMe+R4</option> | |
| 259 <option value="TIMe+R5">TIMe+R5</option> | |
| 260 <option value="TIMe+R6">TIMe+R6</option> | |
| 261 <option value="TIMe+R7">TIMe+R7</option> | |
| 262 <option value="TIMe+R8">TIMe+R8</option> | |
| 263 <option value="TIMe+R9">TIMe+R9</option> | |
| 264 <option value="TIMe+R10">TIMe+R10</option> | |
| 265 <option value="TIM">TIM</option> | |
| 266 <option value="TIM+I">TIM+I</option> | |
| 267 <option value="TIM+G">TIM+G</option> | |
| 268 <option value="TIM+I+G">TIM+I+G</option> | |
| 269 <option value="TIM+R2">TIM+R2</option> | |
| 270 <option value="TIM+R3">TIM+R3</option> | |
| 271 <option value="TIM+R4">TIM+R4</option> | |
| 272 <option value="TIM+R5">TIM+R5</option> | |
| 273 <option value="TIM+R6">TIM+R6</option> | |
| 274 <option value="TIM+R7">TIM+R7</option> | |
| 275 <option value="TIM+R8">TIM+R8</option> | |
| 276 <option value="TIM+R9">TIM+R9</option> | |
| 277 <option value="TIM+R10">TIM+R10</option> | |
| 278 <option value="TIM2e">TIM2e</option> | |
| 279 <option value="TIM2e+I">TIM2e+I</option> | |
| 280 <option value="TIM2e+G">TIM2e+G</option> | |
| 281 <option value="TIM2e+I+G">TIM2e+I+G</option> | |
| 282 <option value="TIM2e+R2">TIM2e+R2</option> | |
| 283 <option value="TIM2e+R3">TIM2e+R3</option> | |
| 284 <option value="TIM2e+R4">TIM2e+R4</option> | |
| 285 <option value="TIM2e+R5">TIM2e+R5</option> | |
| 286 <option value="TIM2e+R6">TIM2e+R6</option> | |
| 287 <option value="TIM2e+R7">TIM2e+R7</option> | |
| 288 <option value="TIM2e+R8">TIM2e+R8</option> | |
| 289 <option value="TIM2e+R9">TIM2e+R9</option> | |
| 290 <option value="TIM2e+R10">TIM2e+R10</option> | |
| 291 <option value="TIM2">TIM2</option> | |
| 292 <option value="TIM2+I">TIM2+I</option> | |
| 293 <option value="TIM2+G">TIM2+G</option> | |
| 294 <option value="TIM2+I+G">TIM2+I+G</option> | |
| 295 <option value="TIM2+R2">TIM2+R2</option> | |
| 296 <option value="TIM2+R3">TIM2+R3</option> | |
| 297 <option value="TIM2+R4">TIM2+R4</option> | |
| 298 <option value="TIM2+R5">TIM2+R5</option> | |
| 299 <option value="TIM2+R6">TIM2+R6</option> | |
| 300 <option value="TIM2+R7">TIM2+R7</option> | |
| 301 <option value="TIM2+R8">TIM2+R8</option> | |
| 302 <option value="TIM2+R9">TIM2+R9</option> | |
| 303 <option value="TIM2+R10">TIM2+R10</option> | |
| 304 <option value="TIM3e">TIM3e</option> | |
| 305 <option value="TIM3e+I">TIM3e+I</option> | |
| 306 <option value="TIM3e+G">TIM3e+G</option> | |
| 307 <option value="TIM3e+I+G">TIM3e+I+G</option> | |
| 308 <option value="TIM3e+R2">TIM3e+R2</option> | |
| 309 <option value="TIM3e+R3">TIM3e+R3</option> | |
| 310 <option value="TIM3e+R4">TIM3e+R4</option> | |
| 311 <option value="TIM3e+R5">TIM3e+R5</option> | |
| 312 <option value="TIM3e+R6">TIM3e+R6</option> | |
| 313 <option value="TIM3e+R7">TIM3e+R7</option> | |
| 314 <option value="TIM3e+R8">TIM3e+R8</option> | |
| 315 <option value="TIM3e+R9">TIM3e+R9</option> | |
| 316 <option value="TIM3e+R10">TIM3e+R10</option> | |
| 317 <option value="TIM3">TIM3</option> | |
| 318 <option value="TIM3+I">TIM3+I</option> | |
| 319 <option value="TIM3+G">TIM3+G</option> | |
| 320 <option value="TIM3+I+G">TIM3+I+G</option> | |
| 321 <option value="TIM3+R2">TIM3+R2</option> | |
| 322 <option value="TIM3+R3">TIM3+R3</option> | |
| 323 <option value="TIM3+R4">TIM3+R4</option> | |
| 324 <option value="TIM3+R5">TIM3+R5</option> | |
| 325 <option value="TIM3+R6">TIM3+R6</option> | |
| 326 <option value="TIM3+R7">TIM3+R7</option> | |
| 327 <option value="TIM3+R8">TIM3+R8</option> | |
| 328 <option value="TIM3+R9">TIM3+R9</option> | |
| 329 <option value="TIM3+R10">TIM3+R10</option> | |
| 330 <option value="TVMe">TVMe</option> | |
| 331 <option value="TVMe+I">TVMe+I</option> | |
| 332 <option value="TVMe+G">TVMe+G</option> | |
| 333 <option value="TVMe+I+G">TVMe+I+G</option> | |
| 334 <option value="TVMe+R2">TVMe+R2</option> | |
| 335 <option value="TVMe+R3">TVMe+R3</option> | |
| 336 <option value="TVMe+R4">TVMe+R4</option> | |
| 337 <option value="TVMe+R5">TVMe+R5</option> | |
| 338 <option value="TVMe+R6">TVMe+R6</option> | |
| 339 <option value="TVMe+R7">TVMe+R7</option> | |
| 340 <option value="TVMe+R8">TVMe+R8</option> | |
| 341 <option value="TVMe+R9">TVMe+R9</option> | |
| 342 <option value="TVMe+R10">TVMe+R10</option> | |
| 343 <option value="TVM">TVM</option> | |
| 344 <option value="TVM+I">TVM+I</option> | |
| 345 <option value="TVM+G">TVM+G</option> | |
| 346 <option value="TVM+I+G">TVM+I+G</option> | |
| 347 <option value="TVM+R2">TVM+R2</option> | |
| 348 <option value="TVM+R3">TVM+R3</option> | |
| 349 <option value="TVM+R4">TVM+R4</option> | |
| 350 <option value="TVM+R5">TVM+R5</option> | |
| 351 <option value="TVM+R6">TVM+R6</option> | |
| 352 <option value="TVM+R7">TVM+R7</option> | |
| 353 <option value="TVM+R8">TVM+R8</option> | |
| 354 <option value="TVM+R9">TVM+R9</option> | |
| 355 <option value="TVM+R10">TVM+R10</option> | |
| 356 <option value="SYM">SYM</option> | |
| 357 <option value="SYM+I">SYM+I</option> | |
| 358 <option value="SYM+G">SYM+G</option> | |
| 359 <option value="SYM+I+G">SYM+I+G</option> | |
| 360 <option value="SYM+R2">SYM+R2</option> | |
| 361 <option value="SYM+R3">SYM+R3</option> | |
| 362 <option value="SYM+R4">SYM+R4</option> | |
| 363 <option value="SYM+R5">SYM+R5</option> | |
| 364 <option value="SYM+R6">SYM+R6</option> | |
| 365 <option value="SYM+R7">SYM+R7</option> | |
| 366 <option value="SYM+R8">SYM+R8</option> | |
| 367 <option value="SYM+R9">SYM+R9</option> | |
| 368 <option value="SYM+R10">SYM+R10</option> | |
| 369 <option value="GTR">GTR</option> | |
| 370 <option value="GTR+I">GTR+I</option> | |
| 371 <option value="GTR+G">GTR+G</option> | |
| 372 <option value="GTR+I+G">GTR+I+G</option> | |
| 373 <option value="GTR+R2">GTR+R2</option> | |
| 374 <option value="GTR+R3">GTR+R3</option> | |
| 375 <option value="GTR+R4">GTR+R4</option> | |
| 376 <option value="GTR+R5">GTR+R5</option> | |
| 377 <option value="GTR+R6">GTR+R6</option> | |
| 378 <option value="GTR+R7">GTR+R7</option> | |
| 379 <option value="GTR+R8">GTR+R8</option> | |
| 380 <option value="GTR+R9">GTR+R9</option> | |
| 381 <option value="GTR+R10">GTR+R10</option> | |
| 382 <option value="MFP">MFP</option> | |
| 383 <option value="TEST">TEST</option> | |
| 384 </param> | |
| 385 <param label="--p-n-init-pars-trees: INTEGER Range(1, None) Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pninitparstrees" optional="False" type="text" /> | |
| 386 <param label="--p-n-top-init-trees: INTEGER Range(1, None) Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pntopinittrees" optional="False" type="text" /> | |
| 387 <param label="--p-n-best-retain-trees: INTEGER Range(1, None) Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnbestretaintrees" optional="False" type="text" /> | |
| 388 <param label="--p-n-iter: INTEGER Fix number of iterations to stop. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="pniter" optional="False" type="text" /> | |
| 389 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="False" type="text" /> | |
| 390 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 1.0) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="False" type="text" /> | |
| 391 <param label="--p-spr-radius: INTEGER Radius for parsimony SPR search. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="psprradius" optional="False" type="text" /> | |
| 392 <param label="--p-allnni: --p-allnni: / --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean" /> | |
| 393 <param label="--p-fast: --p-fast: / --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean" /> | |
| 394 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="palrt" optional="False" type="text" /> | |
| 395 <param label="--p-abayes: --p-abayes: / --p-no-abayes Single branch test method. Approximate Bayes test. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [default: False]" name="pabayes" selected="False" type="boolean" /> | |
| 396 <param label="--p-lbp: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="plbp" optional="False" type="text" /> | |
| 397 <param label="--p-safe: --p-safe: / --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean" /> | |
| 398 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> | |
| 399 | |
| 400 </inputs> | |
| 401 | |
| 402 <outputs> | |
| 403 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" /> | |
| 404 | |
| 405 </outputs> | |
| 406 | |
| 407 <help><![CDATA[ | |
| 408 Construct a phylogenetic tree with IQ-TREE. | |
| 409 ############################################################### | |
| 410 | |
| 411 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with | |
| 412 automatic model selection. | |
| 413 | |
| 414 Parameters | |
| 415 ---------- | |
| 416 alignment : FeatureData[AlignedSequence] | |
| 417 Aligned sequences to be used for phylogenetic reconstruction. | |
| 418 seed : Int, optional | |
| 419 Random number seed. If not set, program defaults will be used. See IQ- | |
| 420 TREE manual for details. | |
| 421 n_cores : Int % Range(1, None) | Str % Choices('auto'), optional | |
| 422 The number of cores to use for parallel processing. Use `auto` to let | |
| 423 IQ-TREE automatically determine the optimal number of cores to use. | |
| 424 n_cores_max : Int % Range(2, None), optional | |
| 425 Limits the maximum number of cores to be used when 'n_cores' is set to | |
| 426 'auto'. | |
| 427 n_runs : Int % Range(1, None), optional | |
| 428 Number of indepedent runs. Multiple independent runs (e.g. 10) can | |
| 429 outperform a single run in terms of likelihood maximisation. | |
| 430 substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional | |
| 431 Model of Nucleotide Substitution. If not provided, IQ-TREE will | |
| 432 determine the best fit substitution model automatically. | |
| 433 n_init_pars_trees : Int % Range(1, None), optional | |
| 434 Number of initial parsimony trees. If not set, program defaults will be | |
| 435 used. See IQ-TREE manual for details. | |
| 436 n_top_init_trees : Int % Range(1, None), optional | |
| 437 Number of top initial trees. If not set, program defaults will be used. | |
| 438 See IQ-TREE manual for details. | |
| 439 n_best_retain_trees : Int % Range(1, None), optional | |
| 440 Number of best trees retained during search. If not set, program | |
| 441 defaults will be used. See IQ-TREE manual for details. | |
| 442 n_iter : Int % Range(1, None), optional | |
| 443 Fix number of iterations to stop. If not set, program defaults will be | |
| 444 used. See IQ-TREE manual for details. | |
| 445 stop_iter : Int % Range(1, None), optional | |
| 446 Number of unsuccessful iterations to stop. If not set, program defaults | |
| 447 will be used. See IQ-TREE manual for details. | |
| 448 perturb_nni_strength : Float % Range(0.01, 1.0), optional | |
| 449 Perturbation strength for randomized NNI. If not set, program defaults | |
| 450 will be used. See IQ-TREE manual for details. | |
| 451 spr_radius : Int % Range(1, None), optional | |
| 452 Radius for parsimony SPR search. If not set, program defaults will be | |
| 453 used. See IQ-TREE manual for details. | |
| 454 allnni : Bool, optional | |
| 455 Perform more thorough NNI search. | |
| 456 fast : Bool, optional | |
| 457 Fast search to resemble FastTree. | |
| 458 alrt : Int % Range(1000, None), optional | |
| 459 Single branch test method. Number of bootstrap replicates to perform an | |
| 460 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 | |
| 461 replicates is recomended. Can be used with other 'single branch test | |
| 462 methods'. Values reported in the order of: alrt, lbp, abayes. | |
| 463 abayes : Bool, optional | |
| 464 Single branch test method. Approximate Bayes test. Can be used with | |
| 465 other 'single branch test methods'. Values reported in the order of: | |
| 466 alrt, lbp, abayes. | |
| 467 lbp : Int % Range(1000, None), optional | |
| 468 Single branch test method. Number of bootstrap replicates to perform a | |
| 469 fast local bootstrap probability method. Minimum of 1000 replicates is | |
| 470 recomended. Can be used with other 'single branch test methods'. Values | |
| 471 reported in the order of: alrt, lbp, abayes. | |
| 472 safe : Bool, optional | |
| 473 Safe likelihood kernel to avoid numerical underflow. | |
| 474 | |
| 475 Returns | |
| 476 ------- | |
| 477 tree : Phylogeny[Unrooted] | |
| 478 The resulting phylogenetic tree. | |
| 479 ]]></help> | |
| 480 <macros> | |
| 481 <import>qiime_citation.xml</import> | |
| 482 </macros> | |
| 483 <expand macro="qiime_citation"/> | |
| 484 </tool> |