|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree" version="2019.4">
|
|
|
3 <description> - Construct a phylogenetic tree with IQ-TREE.</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime phylogeny iqtree
|
|
|
9
|
|
|
10 --i-alignment=$ialignment
|
|
|
11
|
|
|
12 #if str($pseed):
|
|
|
13 --p-seed="$pseed"
|
|
|
14 #end if
|
|
|
15
|
|
|
16 #set $pncores = '${GALAXY_SLOTS:-4}'
|
|
|
17
|
|
|
18 #if str($pncores):
|
|
|
19 --p-n-cores="$pncores"
|
|
|
20 #end if
|
|
|
21
|
|
|
22 #if $pnruns:
|
|
|
23 --p-n-runs=$pnruns
|
|
|
24 #end if
|
|
|
25
|
|
|
26 #if str($psubstitutionmodel) != 'None':
|
|
|
27 --p-substitution-model=$psubstitutionmodel
|
|
|
28 #end if
|
|
|
29
|
|
|
30 #if str($pninitparstrees):
|
|
|
31 --p-n-init-pars-trees="$pninitparstrees"
|
|
|
32 #end if
|
|
|
33
|
|
|
34 #if str($pntopinittrees):
|
|
|
35 --p-n-top-init-trees="$pntopinittrees"
|
|
|
36 #end if
|
|
|
37
|
|
|
38 #if str($pnbestretaintrees):
|
|
|
39 --p-n-best-retain-trees="$pnbestretaintrees"
|
|
|
40 #end if
|
|
|
41
|
|
|
42 #if str($pniter):
|
|
|
43 --p-n-iter="$pniter"
|
|
|
44 #end if
|
|
|
45
|
|
|
46 #if str($pstopiter):
|
|
|
47 --p-stop-iter="$pstopiter"
|
|
|
48 #end if
|
|
|
49
|
|
|
50 #if str($pperturbnnistrength):
|
|
|
51 --p-perturb-nni-strength="$pperturbnnistrength"
|
|
|
52 #end if
|
|
|
53
|
|
|
54 #if str($psprradius):
|
|
|
55 --p-spr-radius="$psprradius"
|
|
|
56 #end if
|
|
|
57
|
|
|
58 #if $pallnni:
|
|
|
59 --p-allnni
|
|
|
60 #end if
|
|
|
61
|
|
|
62 #if $pfast:
|
|
|
63 --p-fast
|
|
|
64 #end if
|
|
|
65
|
|
|
66 #if str($palrt):
|
|
|
67 --p-alrt="$palrt"
|
|
|
68 #end if
|
|
|
69
|
|
|
70 #if $pabayes:
|
|
|
71 --p-abayes
|
|
|
72 #end if
|
|
|
73
|
|
|
74 #if str($plbp):
|
|
|
75 --p-lbp="$plbp"
|
|
|
76 #end if
|
|
|
77
|
|
|
78 #if $psafe:
|
|
|
79 --p-safe
|
|
|
80 #end if
|
|
|
81
|
|
|
82 --o-tree=otree
|
|
|
83 ;
|
|
|
84 cp otree.qza $otree
|
|
|
85 ]]></command>
|
|
|
86 <inputs>
|
|
|
87 <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"/>
|
|
|
88 <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="True" type="integer"/>
|
|
|
89 <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]" name="pnruns" optional="True" type="integer" value="1" min="1"/>
|
|
|
90 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
|
|
|
91 <option selected="True" value="None">Selection is Optional</option>
|
|
|
92 <option value="JC">JC</option>
|
|
|
93 <option value="JC+I">JC+I</option>
|
|
|
94 <option value="JC+G">JC+G</option>
|
|
|
95 <option value="JC+I+G">JC+I+G</option>
|
|
|
96 <option value="JC+R2">JC+R2</option>
|
|
|
97 <option value="JC+R3">JC+R3</option>
|
|
|
98 <option value="JC+R4">JC+R4</option>
|
|
|
99 <option value="JC+R5">JC+R5</option>
|
|
|
100 <option value="JC+R6">JC+R6</option>
|
|
|
101 <option value="JC+R7">JC+R7</option>
|
|
|
102 <option value="JC+R8">JC+R8</option>
|
|
|
103 <option value="JC+R9">JC+R9</option>
|
|
|
104 <option value="JC+R10">JC+R10</option>
|
|
|
105 <option value="F81">F81</option>
|
|
|
106 <option value="F81+I">F81+I</option>
|
|
|
107 <option value="F81+G">F81+G</option>
|
|
|
108 <option value="F81+I+G">F81+I+G</option>
|
|
|
109 <option value="F81+R2">F81+R2</option>
|
|
|
110 <option value="F81+R3">F81+R3</option>
|
|
|
111 <option value="F81+R4">F81+R4</option>
|
|
|
112 <option value="F81+R5">F81+R5</option>
|
|
|
113 <option value="F81+R6">F81+R6</option>
|
|
|
114 <option value="F81+R7">F81+R7</option>
|
|
|
115 <option value="F81+R8">F81+R8</option>
|
|
|
116 <option value="F81+R9">F81+R9</option>
|
|
|
117 <option value="F81+R10">F81+R10</option>
|
|
|
118 <option value="K80">K80</option>
|
|
|
119 <option value="K80+I">K80+I</option>
|
|
|
120 <option value="K80+G">K80+G</option>
|
|
|
121 <option value="K80+I+G">K80+I+G</option>
|
|
|
122 <option value="K80+R2">K80+R2</option>
|
|
|
123 <option value="K80+R3">K80+R3</option>
|
|
|
124 <option value="K80+R4">K80+R4</option>
|
|
|
125 <option value="K80+R5">K80+R5</option>
|
|
|
126 <option value="K80+R6">K80+R6</option>
|
|
|
127 <option value="K80+R7">K80+R7</option>
|
|
|
128 <option value="K80+R8">K80+R8</option>
|
|
|
129 <option value="K80+R9">K80+R9</option>
|
|
|
130 <option value="K80+R10">K80+R10</option>
|
|
|
131 <option value="HKY">HKY</option>
|
|
|
132 <option value="HKY+I">HKY+I</option>
|
|
|
133 <option value="HKY+G">HKY+G</option>
|
|
|
134 <option value="HKY+I+G">HKY+I+G</option>
|
|
|
135 <option value="HKY+R2">HKY+R2</option>
|
|
|
136 <option value="HKY+R3">HKY+R3</option>
|
|
|
137 <option value="HKY+R4">HKY+R4</option>
|
|
|
138 <option value="HKY+R5">HKY+R5</option>
|
|
|
139 <option value="HKY+R6">HKY+R6</option>
|
|
|
140 <option value="HKY+R7">HKY+R7</option>
|
|
|
141 <option value="HKY+R8">HKY+R8</option>
|
|
|
142 <option value="HKY+R9">HKY+R9</option>
|
|
|
143 <option value="HKY+R10">HKY+R10</option>
|
|
|
144 <option value="TNe">TNe</option>
|
|
|
145 <option value="TNe+I">TNe+I</option>
|
|
|
146 <option value="TNe+G">TNe+G</option>
|
|
|
147 <option value="TNe+I+G">TNe+I+G</option>
|
|
|
148 <option value="TNe+R2">TNe+R2</option>
|
|
|
149 <option value="TNe+R3">TNe+R3</option>
|
|
|
150 <option value="TNe+R4">TNe+R4</option>
|
|
|
151 <option value="TNe+R5">TNe+R5</option>
|
|
|
152 <option value="TNe+R6">TNe+R6</option>
|
|
|
153 <option value="TNe+R7">TNe+R7</option>
|
|
|
154 <option value="TNe+R8">TNe+R8</option>
|
|
|
155 <option value="TNe+R9">TNe+R9</option>
|
|
|
156 <option value="TNe+R10">TNe+R10</option>
|
|
|
157 <option value="TN">TN</option>
|
|
|
158 <option value="TN+I">TN+I</option>
|
|
|
159 <option value="TN+G">TN+G</option>
|
|
|
160 <option value="TN+I+G">TN+I+G</option>
|
|
|
161 <option value="TN+R2">TN+R2</option>
|
|
|
162 <option value="TN+R3">TN+R3</option>
|
|
|
163 <option value="TN+R4">TN+R4</option>
|
|
|
164 <option value="TN+R5">TN+R5</option>
|
|
|
165 <option value="TN+R6">TN+R6</option>
|
|
|
166 <option value="TN+R7">TN+R7</option>
|
|
|
167 <option value="TN+R8">TN+R8</option>
|
|
|
168 <option value="TN+R9">TN+R9</option>
|
|
|
169 <option value="TN+R10">TN+R10</option>
|
|
|
170 <option value="K81">K81</option>
|
|
|
171 <option value="K81+I">K81+I</option>
|
|
|
172 <option value="K81+G">K81+G</option>
|
|
|
173 <option value="K81+I+G">K81+I+G</option>
|
|
|
174 <option value="K81+R2">K81+R2</option>
|
|
|
175 <option value="K81+R3">K81+R3</option>
|
|
|
176 <option value="K81+R4">K81+R4</option>
|
|
|
177 <option value="K81+R5">K81+R5</option>
|
|
|
178 <option value="K81+R6">K81+R6</option>
|
|
|
179 <option value="K81+R7">K81+R7</option>
|
|
|
180 <option value="K81+R8">K81+R8</option>
|
|
|
181 <option value="K81+R9">K81+R9</option>
|
|
|
182 <option value="K81+R10">K81+R10</option>
|
|
|
183 <option value="K81u">K81u</option>
|
|
|
184 <option value="K81u+I">K81u+I</option>
|
|
|
185 <option value="K81u+G">K81u+G</option>
|
|
|
186 <option value="K81u+I+G">K81u+I+G</option>
|
|
|
187 <option value="K81u+R2">K81u+R2</option>
|
|
|
188 <option value="K81u+R3">K81u+R3</option>
|
|
|
189 <option value="K81u+R4">K81u+R4</option>
|
|
|
190 <option value="K81u+R5">K81u+R5</option>
|
|
|
191 <option value="K81u+R6">K81u+R6</option>
|
|
|
192 <option value="K81u+R7">K81u+R7</option>
|
|
|
193 <option value="K81u+R8">K81u+R8</option>
|
|
|
194 <option value="K81u+R9">K81u+R9</option>
|
|
|
195 <option value="K81u+R10">K81u+R10</option>
|
|
|
196 <option value="TPM2">TPM2</option>
|
|
|
197 <option value="TPM2+I">TPM2+I</option>
|
|
|
198 <option value="TPM2+G">TPM2+G</option>
|
|
|
199 <option value="TPM2+I+G">TPM2+I+G</option>
|
|
|
200 <option value="TPM2+R2">TPM2+R2</option>
|
|
|
201 <option value="TPM2+R3">TPM2+R3</option>
|
|
|
202 <option value="TPM2+R4">TPM2+R4</option>
|
|
|
203 <option value="TPM2+R5">TPM2+R5</option>
|
|
|
204 <option value="TPM2+R6">TPM2+R6</option>
|
|
|
205 <option value="TPM2+R7">TPM2+R7</option>
|
|
|
206 <option value="TPM2+R8">TPM2+R8</option>
|
|
|
207 <option value="TPM2+R9">TPM2+R9</option>
|
|
|
208 <option value="TPM2+R10">TPM2+R10</option>
|
|
|
209 <option value="TPM2u">TPM2u</option>
|
|
|
210 <option value="TPM2u+I">TPM2u+I</option>
|
|
|
211 <option value="TPM2u+G">TPM2u+G</option>
|
|
|
212 <option value="TPM2u+I+G">TPM2u+I+G</option>
|
|
|
213 <option value="TPM2u+R2">TPM2u+R2</option>
|
|
|
214 <option value="TPM2u+R3">TPM2u+R3</option>
|
|
|
215 <option value="TPM2u+R4">TPM2u+R4</option>
|
|
|
216 <option value="TPM2u+R5">TPM2u+R5</option>
|
|
|
217 <option value="TPM2u+R6">TPM2u+R6</option>
|
|
|
218 <option value="TPM2u+R7">TPM2u+R7</option>
|
|
|
219 <option value="TPM2u+R8">TPM2u+R8</option>
|
|
|
220 <option value="TPM2u+R9">TPM2u+R9</option>
|
|
|
221 <option value="TPM2u+R10">TPM2u+R10</option>
|
|
|
222 <option value="TPM3">TPM3</option>
|
|
|
223 <option value="TPM3+I">TPM3+I</option>
|
|
|
224 <option value="TPM3+G">TPM3+G</option>
|
|
|
225 <option value="TPM3+I+G">TPM3+I+G</option>
|
|
|
226 <option value="TPM3+R2">TPM3+R2</option>
|
|
|
227 <option value="TPM3+R3">TPM3+R3</option>
|
|
|
228 <option value="TPM3+R4">TPM3+R4</option>
|
|
|
229 <option value="TPM3+R5">TPM3+R5</option>
|
|
|
230 <option value="TPM3+R6">TPM3+R6</option>
|
|
|
231 <option value="TPM3+R7">TPM3+R7</option>
|
|
|
232 <option value="TPM3+R8">TPM3+R8</option>
|
|
|
233 <option value="TPM3+R9">TPM3+R9</option>
|
|
|
234 <option value="TPM3+R10">TPM3+R10</option>
|
|
|
235 <option value="TPM3u">TPM3u</option>
|
|
|
236 <option value="TPM3u+I">TPM3u+I</option>
|
|
|
237 <option value="TPM3u+G">TPM3u+G</option>
|
|
|
238 <option value="TPM3u+I+G">TPM3u+I+G</option>
|
|
|
239 <option value="TPM3u+R2">TPM3u+R2</option>
|
|
|
240 <option value="TPM3u+R3">TPM3u+R3</option>
|
|
|
241 <option value="TPM3u+R4">TPM3u+R4</option>
|
|
|
242 <option value="TPM3u+R5">TPM3u+R5</option>
|
|
|
243 <option value="TPM3u+R6">TPM3u+R6</option>
|
|
|
244 <option value="TPM3u+R7">TPM3u+R7</option>
|
|
|
245 <option value="TPM3u+R8">TPM3u+R8</option>
|
|
|
246 <option value="TPM3u+R9">TPM3u+R9</option>
|
|
|
247 <option value="TPM3u+R10">TPM3u+R10</option>
|
|
|
248 <option value="TIMe">TIMe</option>
|
|
|
249 <option value="TIMe+I">TIMe+I</option>
|
|
|
250 <option value="TIMe+G">TIMe+G</option>
|
|
|
251 <option value="TIMe+I+G">TIMe+I+G</option>
|
|
|
252 <option value="TIMe+R2">TIMe+R2</option>
|
|
|
253 <option value="TIMe+R3">TIMe+R3</option>
|
|
|
254 <option value="TIMe+R4">TIMe+R4</option>
|
|
|
255 <option value="TIMe+R5">TIMe+R5</option>
|
|
|
256 <option value="TIMe+R6">TIMe+R6</option>
|
|
|
257 <option value="TIMe+R7">TIMe+R7</option>
|
|
|
258 <option value="TIMe+R8">TIMe+R8</option>
|
|
|
259 <option value="TIMe+R9">TIMe+R9</option>
|
|
|
260 <option value="TIMe+R10">TIMe+R10</option>
|
|
|
261 <option value="TIM">TIM</option>
|
|
|
262 <option value="TIM+I">TIM+I</option>
|
|
|
263 <option value="TIM+G">TIM+G</option>
|
|
|
264 <option value="TIM+I+G">TIM+I+G</option>
|
|
|
265 <option value="TIM+R2">TIM+R2</option>
|
|
|
266 <option value="TIM+R3">TIM+R3</option>
|
|
|
267 <option value="TIM+R4">TIM+R4</option>
|
|
|
268 <option value="TIM+R5">TIM+R5</option>
|
|
|
269 <option value="TIM+R6">TIM+R6</option>
|
|
|
270 <option value="TIM+R7">TIM+R7</option>
|
|
|
271 <option value="TIM+R8">TIM+R8</option>
|
|
|
272 <option value="TIM+R9">TIM+R9</option>
|
|
|
273 <option value="TIM+R10">TIM+R10</option>
|
|
|
274 <option value="TIM2e">TIM2e</option>
|
|
|
275 <option value="TIM2e+I">TIM2e+I</option>
|
|
|
276 <option value="TIM2e+G">TIM2e+G</option>
|
|
|
277 <option value="TIM2e+I+G">TIM2e+I+G</option>
|
|
|
278 <option value="TIM2e+R2">TIM2e+R2</option>
|
|
|
279 <option value="TIM2e+R3">TIM2e+R3</option>
|
|
|
280 <option value="TIM2e+R4">TIM2e+R4</option>
|
|
|
281 <option value="TIM2e+R5">TIM2e+R5</option>
|
|
|
282 <option value="TIM2e+R6">TIM2e+R6</option>
|
|
|
283 <option value="TIM2e+R7">TIM2e+R7</option>
|
|
|
284 <option value="TIM2e+R8">TIM2e+R8</option>
|
|
|
285 <option value="TIM2e+R9">TIM2e+R9</option>
|
|
|
286 <option value="TIM2e+R10">TIM2e+R10</option>
|
|
|
287 <option value="TIM2">TIM2</option>
|
|
|
288 <option value="TIM2+I">TIM2+I</option>
|
|
|
289 <option value="TIM2+G">TIM2+G</option>
|
|
|
290 <option value="TIM2+I+G">TIM2+I+G</option>
|
|
|
291 <option value="TIM2+R2">TIM2+R2</option>
|
|
|
292 <option value="TIM2+R3">TIM2+R3</option>
|
|
|
293 <option value="TIM2+R4">TIM2+R4</option>
|
|
|
294 <option value="TIM2+R5">TIM2+R5</option>
|
|
|
295 <option value="TIM2+R6">TIM2+R6</option>
|
|
|
296 <option value="TIM2+R7">TIM2+R7</option>
|
|
|
297 <option value="TIM2+R8">TIM2+R8</option>
|
|
|
298 <option value="TIM2+R9">TIM2+R9</option>
|
|
|
299 <option value="TIM2+R10">TIM2+R10</option>
|
|
|
300 <option value="TIM3e">TIM3e</option>
|
|
|
301 <option value="TIM3e+I">TIM3e+I</option>
|
|
|
302 <option value="TIM3e+G">TIM3e+G</option>
|
|
|
303 <option value="TIM3e+I+G">TIM3e+I+G</option>
|
|
|
304 <option value="TIM3e+R2">TIM3e+R2</option>
|
|
|
305 <option value="TIM3e+R3">TIM3e+R3</option>
|
|
|
306 <option value="TIM3e+R4">TIM3e+R4</option>
|
|
|
307 <option value="TIM3e+R5">TIM3e+R5</option>
|
|
|
308 <option value="TIM3e+R6">TIM3e+R6</option>
|
|
|
309 <option value="TIM3e+R7">TIM3e+R7</option>
|
|
|
310 <option value="TIM3e+R8">TIM3e+R8</option>
|
|
|
311 <option value="TIM3e+R9">TIM3e+R9</option>
|
|
|
312 <option value="TIM3e+R10">TIM3e+R10</option>
|
|
|
313 <option value="TIM3">TIM3</option>
|
|
|
314 <option value="TIM3+I">TIM3+I</option>
|
|
|
315 <option value="TIM3+G">TIM3+G</option>
|
|
|
316 <option value="TIM3+I+G">TIM3+I+G</option>
|
|
|
317 <option value="TIM3+R2">TIM3+R2</option>
|
|
|
318 <option value="TIM3+R3">TIM3+R3</option>
|
|
|
319 <option value="TIM3+R4">TIM3+R4</option>
|
|
|
320 <option value="TIM3+R5">TIM3+R5</option>
|
|
|
321 <option value="TIM3+R6">TIM3+R6</option>
|
|
|
322 <option value="TIM3+R7">TIM3+R7</option>
|
|
|
323 <option value="TIM3+R8">TIM3+R8</option>
|
|
|
324 <option value="TIM3+R9">TIM3+R9</option>
|
|
|
325 <option value="TIM3+R10">TIM3+R10</option>
|
|
|
326 <option value="TVMe">TVMe</option>
|
|
|
327 <option value="TVMe+I">TVMe+I</option>
|
|
|
328 <option value="TVMe+G">TVMe+G</option>
|
|
|
329 <option value="TVMe+I+G">TVMe+I+G</option>
|
|
|
330 <option value="TVMe+R2">TVMe+R2</option>
|
|
|
331 <option value="TVMe+R3">TVMe+R3</option>
|
|
|
332 <option value="TVMe+R4">TVMe+R4</option>
|
|
|
333 <option value="TVMe+R5">TVMe+R5</option>
|
|
|
334 <option value="TVMe+R6">TVMe+R6</option>
|
|
|
335 <option value="TVMe+R7">TVMe+R7</option>
|
|
|
336 <option value="TVMe+R8">TVMe+R8</option>
|
|
|
337 <option value="TVMe+R9">TVMe+R9</option>
|
|
|
338 <option value="TVMe+R10">TVMe+R10</option>
|
|
|
339 <option value="TVM">TVM</option>
|
|
|
340 <option value="TVM+I">TVM+I</option>
|
|
|
341 <option value="TVM+G">TVM+G</option>
|
|
|
342 <option value="TVM+I+G">TVM+I+G</option>
|
|
|
343 <option value="TVM+R2">TVM+R2</option>
|
|
|
344 <option value="TVM+R3">TVM+R3</option>
|
|
|
345 <option value="TVM+R4">TVM+R4</option>
|
|
|
346 <option value="TVM+R5">TVM+R5</option>
|
|
|
347 <option value="TVM+R6">TVM+R6</option>
|
|
|
348 <option value="TVM+R7">TVM+R7</option>
|
|
|
349 <option value="TVM+R8">TVM+R8</option>
|
|
|
350 <option value="TVM+R9">TVM+R9</option>
|
|
|
351 <option value="TVM+R10">TVM+R10</option>
|
|
|
352 <option value="SYM">SYM</option>
|
|
|
353 <option value="SYM+I">SYM+I</option>
|
|
|
354 <option value="SYM+G">SYM+G</option>
|
|
|
355 <option value="SYM+I+G">SYM+I+G</option>
|
|
|
356 <option value="SYM+R2">SYM+R2</option>
|
|
|
357 <option value="SYM+R3">SYM+R3</option>
|
|
|
358 <option value="SYM+R4">SYM+R4</option>
|
|
|
359 <option value="SYM+R5">SYM+R5</option>
|
|
|
360 <option value="SYM+R6">SYM+R6</option>
|
|
|
361 <option value="SYM+R7">SYM+R7</option>
|
|
|
362 <option value="SYM+R8">SYM+R8</option>
|
|
|
363 <option value="SYM+R9">SYM+R9</option>
|
|
|
364 <option value="SYM+R10">SYM+R10</option>
|
|
|
365 <option value="GTR">GTR</option>
|
|
|
366 <option value="GTR+I">GTR+I</option>
|
|
|
367 <option value="GTR+G">GTR+G</option>
|
|
|
368 <option value="GTR+I+G">GTR+I+G</option>
|
|
|
369 <option value="GTR+R2">GTR+R2</option>
|
|
|
370 <option value="GTR+R3">GTR+R3</option>
|
|
|
371 <option value="GTR+R4">GTR+R4</option>
|
|
|
372 <option value="GTR+R5">GTR+R5</option>
|
|
|
373 <option value="GTR+R6">GTR+R6</option>
|
|
|
374 <option value="GTR+R7">GTR+R7</option>
|
|
|
375 <option value="GTR+R8">GTR+R8</option>
|
|
|
376 <option value="GTR+R9">GTR+R9</option>
|
|
|
377 <option value="GTR+R10">GTR+R10</option>
|
|
|
378 <option value="MFP">MFP</option>
|
|
|
379 <option value="TEST">TEST</option>
|
|
|
380 </param>
|
|
|
381 <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="True" type="integer" min="1"/>
|
|
|
382 <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="True" type="integer" min="1"/>
|
|
|
383 <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="True" type="integer" min="1"/>
|
|
|
384 <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="True" type="integer" min="1"/>
|
|
|
385 <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="True" type="integer" min="1"/>
|
|
|
386 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 99) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="True" type="float" min="0.01" max="99"/>
|
|
|
387 <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="True" type="integer" min="1"/>
|
|
|
388 <param label="--p-allnni: --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean"/>
|
|
|
389 <param label="--p-fast: --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean"/>
|
|
|
390 <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. Set to '0' for parametric aLRT test. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="palrt" optional="True" type="integer" min="1000"/>
|
|
|
391 <param label="--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"/>
|
|
|
392 <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="True" type="integer" min="1000"/>
|
|
|
393 <param label="--p-safe: --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean"/>
|
|
|
394 </inputs>
|
|
|
395 <outputs>
|
|
|
396 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
|
|
|
397 </outputs>
|
|
|
398 <help><![CDATA[
|
|
|
399 Construct a phylogenetic tree with IQ-TREE.
|
|
|
400 ###########################################
|
|
|
401
|
|
|
402 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
|
|
|
403 automatic model selection.
|
|
|
404
|
|
|
405 Parameters
|
|
|
406 ----------
|
|
|
407 alignment : FeatureData[AlignedSequence]
|
|
|
408 Aligned sequences to be used for phylogenetic reconstruction.
|
|
|
409 seed : Int, optional
|
|
|
410 Random number seed. If not set, program defaults will be used. See IQ-
|
|
|
411 TREE manual for details.
|
|
|
412 n_runs : Int % Range(1, None), optional
|
|
|
413 Number of indepedent runs. Multiple independent runs (e.g. 10) can
|
|
|
414 outperform a single run in terms of likelihood maximisation.
|
|
|
415 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
|
|
|
416 Model of Nucleotide Substitution. If not provided, IQ-TREE will
|
|
|
417 determine the best fit substitution model automatically.
|
|
|
418 n_init_pars_trees : Int % Range(1, None), optional
|
|
|
419 Number of initial parsimony trees. If not set, program defaults will be
|
|
|
420 used. See IQ-TREE manual for details.
|
|
|
421 n_top_init_trees : Int % Range(1, None), optional
|
|
|
422 Number of top initial trees. If not set, program defaults will be used.
|
|
|
423 See IQ-TREE manual for details.
|
|
|
424 n_best_retain_trees : Int % Range(1, None), optional
|
|
|
425 Number of best trees retained during search. If not set, program
|
|
|
426 defaults will be used. See IQ-TREE manual for details.
|
|
|
427 n_iter : Int % Range(1, None), optional
|
|
|
428 Fix number of iterations to stop. If not set, program defaults will be
|
|
|
429 used. See IQ-TREE manual for details.
|
|
|
430 stop_iter : Int % Range(1, None), optional
|
|
|
431 Number of unsuccessful iterations to stop. If not set, program defaults
|
|
|
432 will be used. See IQ-TREE manual for details.
|
|
|
433 perturb_nni_strength : Float % Range(0.01, 99), optional
|
|
|
434 Perturbation strength for randomized NNI. If not set, program defaults
|
|
|
435 will be used. See IQ-TREE manual for details.
|
|
|
436 spr_radius : Int % Range(1, None), optional
|
|
|
437 Radius for parsimony SPR search. If not set, program defaults will be
|
|
|
438 used. See IQ-TREE manual for details.
|
|
|
439 allnni : Bool, optional
|
|
|
440 Perform more thorough NNI search.
|
|
|
441 fast : Bool, optional
|
|
|
442 Fast search to resemble FastTree.
|
|
|
443 alrt : Int % Range(1000, None), optional
|
|
|
444 Single branch test method. Number of bootstrap replicates to perform an
|
|
|
445 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
|
|
|
446 replicates is recomended. Set to '0' for parametric aLRT test. Can be
|
|
|
447 used with other 'single branch test methods'. Values reported in the
|
|
|
448 order of: alrt, lbp, abayes.
|
|
|
449 abayes : Bool, optional
|
|
|
450 Single branch test method. Approximate Bayes test. Can be used with
|
|
|
451 other 'single branch test methods'. Values reported in the order of:
|
|
|
452 alrt, lbp, abayes.
|
|
|
453 lbp : Int % Range(1000, None), optional
|
|
|
454 Single branch test method. Number of bootstrap replicates to perform a
|
|
|
455 fast local bootstrap probability method. Minimum of 1000 replicates is
|
|
|
456 recomended. Can be used with other 'single branch test methods'. Values
|
|
|
457 reported in the order of: alrt, lbp, abayes.
|
|
|
458 safe : Bool, optional
|
|
|
459 Safe likelihood kernel to avoid numerical underflow.
|
|
|
460
|
|
|
461 Returns
|
|
|
462 -------
|
|
|
463 tree : Phylogeny[Unrooted]
|
|
|
464 The resulting phylogenetic tree.
|
|
|
465 ]]></help>
|
|
|
466 <macros>
|
|
|
467 <import>qiime_citation.xml</import>
|
|
|
468 </macros>
|
|
|
469 <expand macro="qiime_citation"/>
|
|
|
470 </tool>
|
