|
14
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_phylogeny_align-to-tree-mafft-iqtree" name="qiime phylogeny align-to-tree-mafft-iqtree"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Build a phylogenetic tree using iqtree and mafft alignment.</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime phylogeny align-to-tree-mafft-iqtree
|
|
|
10
|
|
|
11 --i-sequences=$isequences
|
|
|
12
|
|
|
13 #if str($pnthreads) != 'None':
|
|
|
14 --p-n-threads=$pnthreads
|
|
|
15 #end if
|
|
|
16
|
|
|
17 --p-mask-max-gap-frequency=$pmaskmaxgapfrequency
|
|
|
18
|
|
|
19 --p-mask-min-conservation=$pmaskminconservation
|
|
|
20
|
|
|
21 #if str($psubstitutionmodel) != 'None':
|
|
|
22 --p-substitution-model=$psubstitutionmodel
|
|
|
23 #end if
|
|
|
24
|
|
|
25 #if $pfast:
|
|
|
26 --p-fast
|
|
|
27 #end if
|
|
|
28
|
|
|
29 #if str($palrt):
|
|
|
30 --p-alrt=$palrt
|
|
|
31 #end if
|
|
|
32 #if str($pseed):
|
|
|
33 --p-seed=$pseed
|
|
|
34 #end if
|
|
|
35 #if str($pstopiter):
|
|
|
36 --p-stop-iter=$pstopiter
|
|
|
37 #end if
|
|
|
38 #if str($pperturbnnistrength):
|
|
|
39 --p-perturb-nni-strength=$pperturbnnistrength
|
|
|
40 #end if
|
|
|
41 --o-alignment=oalignment
|
|
|
42
|
|
|
43 --o-masked-alignment=omaskedalignment
|
|
|
44
|
|
|
45 --o-tree=otree
|
|
|
46
|
|
|
47 --o-rooted-tree=orootedtree
|
|
|
48
|
|
|
49 #if str($examples) != 'None':
|
|
|
50 --examples=$examples
|
|
|
51 #end if
|
|
|
52
|
|
|
53 ;
|
|
|
54 cp orootedtree.qza $orootedtree
|
|
|
55
|
|
|
56 ]]></command>
|
|
|
57 <inputs>
|
|
|
58 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data" />
|
|
|
59 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
|
|
|
60 <option selected="True" value="None">Selection is Optional</option>
|
|
|
61 <option value="Int % Range(1">Int % Range(1</option>
|
|
|
62 <option value="None">None</option>
|
|
|
63 </param>
|
|
|
64 <param exclude_max="False" label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" />
|
|
|
65 <param exclude_max="False" label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" />
|
|
|
66 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
|
|
|
67 <option selected="True" value="None">Selection is Optional</option>
|
|
|
68 <option value="JC">JC</option>
|
|
|
69 <option value="JC+I">JC+I</option>
|
|
|
70 <option value="JC+G">JC+G</option>
|
|
|
71 <option value="JC+I+G">JC+I+G</option>
|
|
|
72 <option value="JC+R2">JC+R2</option>
|
|
|
73 <option value="JC+R3">JC+R3</option>
|
|
|
74 <option value="JC+R4">JC+R4</option>
|
|
|
75 <option value="JC+R5">JC+R5</option>
|
|
|
76 <option value="JC+R6">JC+R6</option>
|
|
|
77 <option value="JC+R7">JC+R7</option>
|
|
|
78 <option value="JC+R8">JC+R8</option>
|
|
|
79 <option value="JC+R9">JC+R9</option>
|
|
|
80 <option value="JC+R10">JC+R10</option>
|
|
|
81 <option value="F81">F81</option>
|
|
|
82 <option value="F81+I">F81+I</option>
|
|
|
83 <option value="F81+G">F81+G</option>
|
|
|
84 <option value="F81+I+G">F81+I+G</option>
|
|
|
85 <option value="F81+R2">F81+R2</option>
|
|
|
86 <option value="F81+R3">F81+R3</option>
|
|
|
87 <option value="F81+R4">F81+R4</option>
|
|
|
88 <option value="F81+R5">F81+R5</option>
|
|
|
89 <option value="F81+R6">F81+R6</option>
|
|
|
90 <option value="F81+R7">F81+R7</option>
|
|
|
91 <option value="F81+R8">F81+R8</option>
|
|
|
92 <option value="F81+R9">F81+R9</option>
|
|
|
93 <option value="F81+R10">F81+R10</option>
|
|
|
94 <option value="K80">K80</option>
|
|
|
95 <option value="K80+I">K80+I</option>
|
|
|
96 <option value="K80+G">K80+G</option>
|
|
|
97 <option value="K80+I+G">K80+I+G</option>
|
|
|
98 <option value="K80+R2">K80+R2</option>
|
|
|
99 <option value="K80+R3">K80+R3</option>
|
|
|
100 <option value="K80+R4">K80+R4</option>
|
|
|
101 <option value="K80+R5">K80+R5</option>
|
|
|
102 <option value="K80+R6">K80+R6</option>
|
|
|
103 <option value="K80+R7">K80+R7</option>
|
|
|
104 <option value="K80+R8">K80+R8</option>
|
|
|
105 <option value="K80+R9">K80+R9</option>
|
|
|
106 <option value="K80+R10">K80+R10</option>
|
|
|
107 <option value="HKY">HKY</option>
|
|
|
108 <option value="HKY+I">HKY+I</option>
|
|
|
109 <option value="HKY+G">HKY+G</option>
|
|
|
110 <option value="HKY+I+G">HKY+I+G</option>
|
|
|
111 <option value="HKY+R2">HKY+R2</option>
|
|
|
112 <option value="HKY+R3">HKY+R3</option>
|
|
|
113 <option value="HKY+R4">HKY+R4</option>
|
|
|
114 <option value="HKY+R5">HKY+R5</option>
|
|
|
115 <option value="HKY+R6">HKY+R6</option>
|
|
|
116 <option value="HKY+R7">HKY+R7</option>
|
|
|
117 <option value="HKY+R8">HKY+R8</option>
|
|
|
118 <option value="HKY+R9">HKY+R9</option>
|
|
|
119 <option value="HKY+R10">HKY+R10</option>
|
|
|
120 <option value="TNe">TNe</option>
|
|
|
121 <option value="TNe+I">TNe+I</option>
|
|
|
122 <option value="TNe+G">TNe+G</option>
|
|
|
123 <option value="TNe+I+G">TNe+I+G</option>
|
|
|
124 <option value="TNe+R2">TNe+R2</option>
|
|
|
125 <option value="TNe+R3">TNe+R3</option>
|
|
|
126 <option value="TNe+R4">TNe+R4</option>
|
|
|
127 <option value="TNe+R5">TNe+R5</option>
|
|
|
128 <option value="TNe+R6">TNe+R6</option>
|
|
|
129 <option value="TNe+R7">TNe+R7</option>
|
|
|
130 <option value="TNe+R8">TNe+R8</option>
|
|
|
131 <option value="TNe+R9">TNe+R9</option>
|
|
|
132 <option value="TNe+R10">TNe+R10</option>
|
|
|
133 <option value="TN">TN</option>
|
|
|
134 <option value="TN+I">TN+I</option>
|
|
|
135 <option value="TN+G">TN+G</option>
|
|
|
136 <option value="TN+I+G">TN+I+G</option>
|
|
|
137 <option value="TN+R2">TN+R2</option>
|
|
|
138 <option value="TN+R3">TN+R3</option>
|
|
|
139 <option value="TN+R4">TN+R4</option>
|
|
|
140 <option value="TN+R5">TN+R5</option>
|
|
|
141 <option value="TN+R6">TN+R6</option>
|
|
|
142 <option value="TN+R7">TN+R7</option>
|
|
|
143 <option value="TN+R8">TN+R8</option>
|
|
|
144 <option value="TN+R9">TN+R9</option>
|
|
|
145 <option value="TN+R10">TN+R10</option>
|
|
|
146 <option value="K81">K81</option>
|
|
|
147 <option value="K81+I">K81+I</option>
|
|
|
148 <option value="K81+G">K81+G</option>
|
|
|
149 <option value="K81+I+G">K81+I+G</option>
|
|
|
150 <option value="K81+R2">K81+R2</option>
|
|
|
151 <option value="K81+R3">K81+R3</option>
|
|
|
152 <option value="K81+R4">K81+R4</option>
|
|
|
153 <option value="K81+R5">K81+R5</option>
|
|
|
154 <option value="K81+R6">K81+R6</option>
|
|
|
155 <option value="K81+R7">K81+R7</option>
|
|
|
156 <option value="K81+R8">K81+R8</option>
|
|
|
157 <option value="K81+R9">K81+R9</option>
|
|
|
158 <option value="K81+R10">K81+R10</option>
|
|
|
159 <option value="K81u">K81u</option>
|
|
|
160 <option value="K81u+I">K81u+I</option>
|
|
|
161 <option value="K81u+G">K81u+G</option>
|
|
|
162 <option value="K81u+I+G">K81u+I+G</option>
|
|
|
163 <option value="K81u+R2">K81u+R2</option>
|
|
|
164 <option value="K81u+R3">K81u+R3</option>
|
|
|
165 <option value="K81u+R4">K81u+R4</option>
|
|
|
166 <option value="K81u+R5">K81u+R5</option>
|
|
|
167 <option value="K81u+R6">K81u+R6</option>
|
|
|
168 <option value="K81u+R7">K81u+R7</option>
|
|
|
169 <option value="K81u+R8">K81u+R8</option>
|
|
|
170 <option value="K81u+R9">K81u+R9</option>
|
|
|
171 <option value="K81u+R10">K81u+R10</option>
|
|
|
172 <option value="TPM2">TPM2</option>
|
|
|
173 <option value="TPM2+I">TPM2+I</option>
|
|
|
174 <option value="TPM2+G">TPM2+G</option>
|
|
|
175 <option value="TPM2+I+G">TPM2+I+G</option>
|
|
|
176 <option value="TPM2+R2">TPM2+R2</option>
|
|
|
177 <option value="TPM2+R3">TPM2+R3</option>
|
|
|
178 <option value="TPM2+R4">TPM2+R4</option>
|
|
|
179 <option value="TPM2+R5">TPM2+R5</option>
|
|
|
180 <option value="TPM2+R6">TPM2+R6</option>
|
|
|
181 <option value="TPM2+R7">TPM2+R7</option>
|
|
|
182 <option value="TPM2+R8">TPM2+R8</option>
|
|
|
183 <option value="TPM2+R9">TPM2+R9</option>
|
|
|
184 <option value="TPM2+R10">TPM2+R10</option>
|
|
|
185 <option value="TPM2u">TPM2u</option>
|
|
|
186 <option value="TPM2u+I">TPM2u+I</option>
|
|
|
187 <option value="TPM2u+G">TPM2u+G</option>
|
|
|
188 <option value="TPM2u+I+G">TPM2u+I+G</option>
|
|
|
189 <option value="TPM2u+R2">TPM2u+R2</option>
|
|
|
190 <option value="TPM2u+R3">TPM2u+R3</option>
|
|
|
191 <option value="TPM2u+R4">TPM2u+R4</option>
|
|
|
192 <option value="TPM2u+R5">TPM2u+R5</option>
|
|
|
193 <option value="TPM2u+R6">TPM2u+R6</option>
|
|
|
194 <option value="TPM2u+R7">TPM2u+R7</option>
|
|
|
195 <option value="TPM2u+R8">TPM2u+R8</option>
|
|
|
196 <option value="TPM2u+R9">TPM2u+R9</option>
|
|
|
197 <option value="TPM2u+R10">TPM2u+R10</option>
|
|
|
198 <option value="TPM3">TPM3</option>
|
|
|
199 <option value="TPM3+I">TPM3+I</option>
|
|
|
200 <option value="TPM3+G">TPM3+G</option>
|
|
|
201 <option value="TPM3+I+G">TPM3+I+G</option>
|
|
|
202 <option value="TPM3+R2">TPM3+R2</option>
|
|
|
203 <option value="TPM3+R3">TPM3+R3</option>
|
|
|
204 <option value="TPM3+R4">TPM3+R4</option>
|
|
|
205 <option value="TPM3+R5">TPM3+R5</option>
|
|
|
206 <option value="TPM3+R6">TPM3+R6</option>
|
|
|
207 <option value="TPM3+R7">TPM3+R7</option>
|
|
|
208 <option value="TPM3+R8">TPM3+R8</option>
|
|
|
209 <option value="TPM3+R9">TPM3+R9</option>
|
|
|
210 <option value="TPM3+R10">TPM3+R10</option>
|
|
|
211 <option value="TPM3u">TPM3u</option>
|
|
|
212 <option value="TPM3u+I">TPM3u+I</option>
|
|
|
213 <option value="TPM3u+G">TPM3u+G</option>
|
|
|
214 <option value="TPM3u+I+G">TPM3u+I+G</option>
|
|
|
215 <option value="TPM3u+R2">TPM3u+R2</option>
|
|
|
216 <option value="TPM3u+R3">TPM3u+R3</option>
|
|
|
217 <option value="TPM3u+R4">TPM3u+R4</option>
|
|
|
218 <option value="TPM3u+R5">TPM3u+R5</option>
|
|
|
219 <option value="TPM3u+R6">TPM3u+R6</option>
|
|
|
220 <option value="TPM3u+R7">TPM3u+R7</option>
|
|
|
221 <option value="TPM3u+R8">TPM3u+R8</option>
|
|
|
222 <option value="TPM3u+R9">TPM3u+R9</option>
|
|
|
223 <option value="TPM3u+R10">TPM3u+R10</option>
|
|
|
224 <option value="TIMe">TIMe</option>
|
|
|
225 <option value="TIMe+I">TIMe+I</option>
|
|
|
226 <option value="TIMe+G">TIMe+G</option>
|
|
|
227 <option value="TIMe+I+G">TIMe+I+G</option>
|
|
|
228 <option value="TIMe+R2">TIMe+R2</option>
|
|
|
229 <option value="TIMe+R3">TIMe+R3</option>
|
|
|
230 <option value="TIMe+R4">TIMe+R4</option>
|
|
|
231 <option value="TIMe+R5">TIMe+R5</option>
|
|
|
232 <option value="TIMe+R6">TIMe+R6</option>
|
|
|
233 <option value="TIMe+R7">TIMe+R7</option>
|
|
|
234 <option value="TIMe+R8">TIMe+R8</option>
|
|
|
235 <option value="TIMe+R9">TIMe+R9</option>
|
|
|
236 <option value="TIMe+R10">TIMe+R10</option>
|
|
|
237 <option value="TIM">TIM</option>
|
|
|
238 <option value="TIM+I">TIM+I</option>
|
|
|
239 <option value="TIM+G">TIM+G</option>
|
|
|
240 <option value="TIM+I+G">TIM+I+G</option>
|
|
|
241 <option value="TIM+R2">TIM+R2</option>
|
|
|
242 <option value="TIM+R3">TIM+R3</option>
|
|
|
243 <option value="TIM+R4">TIM+R4</option>
|
|
|
244 <option value="TIM+R5">TIM+R5</option>
|
|
|
245 <option value="TIM+R6">TIM+R6</option>
|
|
|
246 <option value="TIM+R7">TIM+R7</option>
|
|
|
247 <option value="TIM+R8">TIM+R8</option>
|
|
|
248 <option value="TIM+R9">TIM+R9</option>
|
|
|
249 <option value="TIM+R10">TIM+R10</option>
|
|
|
250 <option value="TIM2e">TIM2e</option>
|
|
|
251 <option value="TIM2e+I">TIM2e+I</option>
|
|
|
252 <option value="TIM2e+G">TIM2e+G</option>
|
|
|
253 <option value="TIM2e+I+G">TIM2e+I+G</option>
|
|
|
254 <option value="TIM2e+R2">TIM2e+R2</option>
|
|
|
255 <option value="TIM2e+R3">TIM2e+R3</option>
|
|
|
256 <option value="TIM2e+R4">TIM2e+R4</option>
|
|
|
257 <option value="TIM2e+R5">TIM2e+R5</option>
|
|
|
258 <option value="TIM2e+R6">TIM2e+R6</option>
|
|
|
259 <option value="TIM2e+R7">TIM2e+R7</option>
|
|
|
260 <option value="TIM2e+R8">TIM2e+R8</option>
|
|
|
261 <option value="TIM2e+R9">TIM2e+R9</option>
|
|
|
262 <option value="TIM2e+R10">TIM2e+R10</option>
|
|
|
263 <option value="TIM2">TIM2</option>
|
|
|
264 <option value="TIM2+I">TIM2+I</option>
|
|
|
265 <option value="TIM2+G">TIM2+G</option>
|
|
|
266 <option value="TIM2+I+G">TIM2+I+G</option>
|
|
|
267 <option value="TIM2+R2">TIM2+R2</option>
|
|
|
268 <option value="TIM2+R3">TIM2+R3</option>
|
|
|
269 <option value="TIM2+R4">TIM2+R4</option>
|
|
|
270 <option value="TIM2+R5">TIM2+R5</option>
|
|
|
271 <option value="TIM2+R6">TIM2+R6</option>
|
|
|
272 <option value="TIM2+R7">TIM2+R7</option>
|
|
|
273 <option value="TIM2+R8">TIM2+R8</option>
|
|
|
274 <option value="TIM2+R9">TIM2+R9</option>
|
|
|
275 <option value="TIM2+R10">TIM2+R10</option>
|
|
|
276 <option value="TIM3e">TIM3e</option>
|
|
|
277 <option value="TIM3e+I">TIM3e+I</option>
|
|
|
278 <option value="TIM3e+G">TIM3e+G</option>
|
|
|
279 <option value="TIM3e+I+G">TIM3e+I+G</option>
|
|
|
280 <option value="TIM3e+R2">TIM3e+R2</option>
|
|
|
281 <option value="TIM3e+R3">TIM3e+R3</option>
|
|
|
282 <option value="TIM3e+R4">TIM3e+R4</option>
|
|
|
283 <option value="TIM3e+R5">TIM3e+R5</option>
|
|
|
284 <option value="TIM3e+R6">TIM3e+R6</option>
|
|
|
285 <option value="TIM3e+R7">TIM3e+R7</option>
|
|
|
286 <option value="TIM3e+R8">TIM3e+R8</option>
|
|
|
287 <option value="TIM3e+R9">TIM3e+R9</option>
|
|
|
288 <option value="TIM3e+R10">TIM3e+R10</option>
|
|
|
289 <option value="TIM3">TIM3</option>
|
|
|
290 <option value="TIM3+I">TIM3+I</option>
|
|
|
291 <option value="TIM3+G">TIM3+G</option>
|
|
|
292 <option value="TIM3+I+G">TIM3+I+G</option>
|
|
|
293 <option value="TIM3+R2">TIM3+R2</option>
|
|
|
294 <option value="TIM3+R3">TIM3+R3</option>
|
|
|
295 <option value="TIM3+R4">TIM3+R4</option>
|
|
|
296 <option value="TIM3+R5">TIM3+R5</option>
|
|
|
297 <option value="TIM3+R6">TIM3+R6</option>
|
|
|
298 <option value="TIM3+R7">TIM3+R7</option>
|
|
|
299 <option value="TIM3+R8">TIM3+R8</option>
|
|
|
300 <option value="TIM3+R9">TIM3+R9</option>
|
|
|
301 <option value="TIM3+R10">TIM3+R10</option>
|
|
|
302 <option value="TVMe">TVMe</option>
|
|
|
303 <option value="TVMe+I">TVMe+I</option>
|
|
|
304 <option value="TVMe+G">TVMe+G</option>
|
|
|
305 <option value="TVMe+I+G">TVMe+I+G</option>
|
|
|
306 <option value="TVMe+R2">TVMe+R2</option>
|
|
|
307 <option value="TVMe+R3">TVMe+R3</option>
|
|
|
308 <option value="TVMe+R4">TVMe+R4</option>
|
|
|
309 <option value="TVMe+R5">TVMe+R5</option>
|
|
|
310 <option value="TVMe+R6">TVMe+R6</option>
|
|
|
311 <option value="TVMe+R7">TVMe+R7</option>
|
|
|
312 <option value="TVMe+R8">TVMe+R8</option>
|
|
|
313 <option value="TVMe+R9">TVMe+R9</option>
|
|
|
314 <option value="TVMe+R10">TVMe+R10</option>
|
|
|
315 <option value="TVM">TVM</option>
|
|
|
316 <option value="TVM+I">TVM+I</option>
|
|
|
317 <option value="TVM+G">TVM+G</option>
|
|
|
318 <option value="TVM+I+G">TVM+I+G</option>
|
|
|
319 <option value="TVM+R2">TVM+R2</option>
|
|
|
320 <option value="TVM+R3">TVM+R3</option>
|
|
|
321 <option value="TVM+R4">TVM+R4</option>
|
|
|
322 <option value="TVM+R5">TVM+R5</option>
|
|
|
323 <option value="TVM+R6">TVM+R6</option>
|
|
|
324 <option value="TVM+R7">TVM+R7</option>
|
|
|
325 <option value="TVM+R8">TVM+R8</option>
|
|
|
326 <option value="TVM+R9">TVM+R9</option>
|
|
|
327 <option value="TVM+R10">TVM+R10</option>
|
|
|
328 <option value="SYM">SYM</option>
|
|
|
329 <option value="SYM+I">SYM+I</option>
|
|
|
330 <option value="SYM+G">SYM+G</option>
|
|
|
331 <option value="SYM+I+G">SYM+I+G</option>
|
|
|
332 <option value="SYM+R2">SYM+R2</option>
|
|
|
333 <option value="SYM+R3">SYM+R3</option>
|
|
|
334 <option value="SYM+R4">SYM+R4</option>
|
|
|
335 <option value="SYM+R5">SYM+R5</option>
|
|
|
336 <option value="SYM+R6">SYM+R6</option>
|
|
|
337 <option value="SYM+R7">SYM+R7</option>
|
|
|
338 <option value="SYM+R8">SYM+R8</option>
|
|
|
339 <option value="SYM+R9">SYM+R9</option>
|
|
|
340 <option value="SYM+R10">SYM+R10</option>
|
|
|
341 <option value="GTR">GTR</option>
|
|
|
342 <option value="GTR+I">GTR+I</option>
|
|
|
343 <option value="GTR+G">GTR+G</option>
|
|
|
344 <option value="GTR+I+G">GTR+I+G</option>
|
|
|
345 <option value="GTR+R2">GTR+R2</option>
|
|
|
346 <option value="GTR+R3">GTR+R3</option>
|
|
|
347 <option value="GTR+R4">GTR+R4</option>
|
|
|
348 <option value="GTR+R5">GTR+R5</option>
|
|
|
349 <option value="GTR+R6">GTR+R6</option>
|
|
|
350 <option value="GTR+R7">GTR+R7</option>
|
|
|
351 <option value="GTR+R8">GTR+R8</option>
|
|
|
352 <option value="GTR+R9">GTR+R9</option>
|
|
|
353 <option value="GTR+R10">GTR+R10</option>
|
|
|
354 <option value="MFP">MFP</option>
|
|
|
355 <option value="TEST">TEST</option>
|
|
|
356 </param>
|
|
|
357 <param label="--p-fast: --p-fast: / --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean" />
|
|
|
358 <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. [optional]" name="palrt" optional="False" type="text" />
|
|
|
359 <param label="--p-seed: INTEGER Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
|
|
|
360 <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" />
|
|
|
361 <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" />
|
|
|
362 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
363
|
|
|
364 </inputs>
|
|
|
365
|
|
|
366 <outputs>
|
|
|
367 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
|
|
|
368 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
|
|
|
369 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
|
|
|
370 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
|
|
|
371
|
|
|
372 </outputs>
|
|
|
373
|
|
|
374 <help><![CDATA[
|
|
|
375 Build a phylogenetic tree using iqtree and mafft alignment.
|
|
|
376 ###############################################################
|
|
|
377
|
|
|
378 This pipeline will start by creating a sequence alignment using MAFFT,
|
|
|
379 after which any alignment columns that are phylogenetically uninformative
|
|
|
380 or ambiguously aligned will be removed (masked). The resulting masked
|
|
|
381 alignment will be used to infer a phylogenetic tree using IQ-TREE. By
|
|
|
382 default the best fit substitution model will be determined by ModelFinder
|
|
|
383 prior to phylogenetic inference. The resulting tree will be subsequently
|
|
|
384 rooted at its midpoint. Output files from each step of the pipeline will be
|
|
|
385 saved. This includes both the unmasked and masked MAFFT alignment from
|
|
|
386 q2-alignment methods, and both the rooted and unrooted phylogenies from
|
|
|
387 q2-phylogeny methods.
|
|
|
388
|
|
|
389 Parameters
|
|
|
390 ----------
|
|
|
391 sequences : FeatureData[Sequence]
|
|
|
392 The sequences to be used for creating a iqtree based rooted
|
|
|
393 phylogenetic tree.
|
|
|
394 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
|
|
|
395 The number of threads. (Use 0 to automatically use all available cores
|
|
|
396 This value is used when aligning the sequences and creating the tree
|
|
|
397 with iqtree.
|
|
|
398 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
|
|
|
399 The maximum relative frequency of gap characters in a column for the
|
|
|
400 column to be retained. This relative frequency must be a number between
|
|
|
401 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
|
|
|
402 gap characters, and 1.0 retains all columns regardless of gap
|
|
|
403 character frequency. This value is used when masking the aligned
|
|
|
404 sequences.
|
|
|
405 mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
|
|
|
406 The minimum relative frequency of at least one non-gap character in a
|
|
|
407 column for that column to be retained. This relative frequency must be
|
|
|
408 a number between 0.0 and 1.0 (inclusive). For example, if a value of
|
|
|
409 0.4 is provided, a column will only be retained if it contains at
|
|
|
410 least one character that is present in at least 40% of the sequences.
|
|
|
411 This value is used when masking the aligned sequences.
|
|
|
412 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
|
|
|
413 Model of Nucleotide Substitution. If not provided, IQ-TREE will
|
|
|
414 determine the best fit substitution model automatically.
|
|
|
415 fast : Bool, optional
|
|
|
416 Fast search to resemble FastTree.
|
|
|
417 alrt : Int % Range(1000, None), optional
|
|
|
418 Single branch test method. Number of bootstrap replicates to perform an
|
|
|
419 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
|
|
|
420 replicates is recomended.
|
|
|
421 seed : Int, optional
|
|
|
422 Random number seed for the iqtree parsimony starting tree. This allows
|
|
|
423 you to reproduce tree results. If not supplied then one will be
|
|
|
424 randomly chosen.
|
|
|
425 stop_iter : Int % Range(1, None), optional
|
|
|
426 Number of unsuccessful iterations to stop. If not set, program defaults
|
|
|
427 will be used. See IQ-TREE manual for details.
|
|
|
428 perturb_nni_strength : Float % Range(0.01, 1.0), optional
|
|
|
429 Perturbation strength for randomized NNI. If not set, program defaults
|
|
|
430 will be used. See IQ-TREE manual for details.
|
|
|
431
|
|
|
432 Returns
|
|
|
433 -------
|
|
|
434 alignment : FeatureData[AlignedSequence]
|
|
|
435 The aligned sequences.
|
|
|
436 masked_alignment : FeatureData[AlignedSequence]
|
|
|
437 The masked alignment.
|
|
|
438 tree : Phylogeny[Unrooted]
|
|
|
439 The unrooted phylogenetic tree.
|
|
|
440 rooted_tree : Phylogeny[Rooted]
|
|
|
441 The rooted phylogenetic tree.
|
|
|
442 ]]></help>
|
|
|
443 <macros>
|
|
|
444 <import>qiime_citation.xml</import>
|
|
|
445 </macros>
|
|
|
446 <expand macro="qiime_citation"/>
|
|
|
447 </tool> |
