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date Mon, 16 Apr 2018 09:00:15 -0400
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1 <tool id="fastme" name="FastME" version="2.0.0">
2 <description>Distance-based inference of phylogenetic trees</description>
3 <requirements>
4 <requirement type="package" version="2.1.5">fastme</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" />
8 </stdio>
9 <version_command>
10 <![CDATA[ fastme --version ]]>
11 </version_command>
12 <command>fastme -f 6
13 --input_data=$input
14 --output_tree=$outputTree
15 --output_matrix=$outputMatrix
16 --output_info=$outputLog
17 --nb_threads=\${GALAXY_SLOTS:-1}
18
19 #if $typeChoice.datatype =="d"
20 --dna=$typeChoice.modeldna
21
22 #else if $typeChoice.datatype =="p"
23 --protein=$typeChoice.modelprot
24
25 #else if $typeChoice.datatype =="cfg":
26 ## Read information of sequence type
27 ## read an info file to choose which option set and set a model by default
28 #set $info = open( str($input_info) ).read()
29 #if 'dna' in $info:
30 --dna=T
31 #else if 'protein' in $info:
32 --protein=L
33 #end if
34 #end if
35
36 #if $gammaChoice.gamma == "true"
37 --gamma=$gammaChoice.rate
38 #end if
39
40 $distance
41 $equilibrium
42 $removeGap
43 $treeRefinement
44
45 #if $bootChoice.boot == "true"
46 --output_boot=$outputBoostrap
47 --bootstrap=$bootChoice.replicates
48 #end if
49
50 >> tmp_stdout;
51 cat tmp_stdout > $outputLog;
52
53 </command>
54 <inputs>
55 <param name="input" type="data" format="phylip, phy" label="Fastme input" help="Phylip Alignment or Matrix file"/>
56 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
57 <conditional name="typeChoice">
58 <param name="datatype" type="select" display="radio" label="Data type" >
59 <option value="d">DNA</option>
60 <option value="p">Protein</option>
61 <option value="m">Matrix</option>
62 <option value="cfg">Config file</option>
63 </param>
64 <when value="d">
65 <param name="modeldna" type="select" label="Evolutionary model">
66 <option value="4">F84</option>
67 <option value="R">RY</option>
68 <option value="1">F81</option>
69 <option value="J">JC69</option>
70 <option value="K">K2P</option>
71 <option value="T" selected="true">TN93</option>
72 <option value="p">p-distance</option>
73 </param>
74 </when>
75 <when value="p">
76 <param name="modelprot" type="select" label="Evolutionary model">
77 <option value="L">LG</option>
78 <option value="W">WAG</option>
79 <option value="J">JTT</option>
80 <option value="h">Day off</option>
81 <option value="C">CpRev</option>
82 <option value="D">DCMut</option>
83 <option value="b">HIVb</option>
84 <option value="I">HIVw</option>
85 <option value="M">MtREV</option>
86 <option value="R">RtREV</option>
87 <option value="p">p-distance</option>
88 </param>
89 </when>
90 <when value="m"/>
91 <when value="cfg">
92 <param name="input_info" format="txt" type="data" multiple="false" label="Config file" help="Precompute file containning sequence description (dna or protein)"/>
93 </when>
94 </conditional>
95 <param name="equilibrium" type="boolean" label="Equilibrium frequencies" truevalue="--equilibrium" falsevalue="" help="By default, frequencies are globally counted from the nucleotides alignment or defined by the proteic substitution model. By checking the box, frequencies are pairwise estimated by counting the nucleotides or estimated by counting the amino-acids in the alignment."/>
96 <conditional name="gammaChoice">
97 <param name="gamma" type="select" label="Gamma distributed rates across sites">
98 <option value="true">Yes</option>
99 <option value="false">No</option>
100 </param>
101 <when value="true">
102 <param name="rate" type="float" label="Gamma distribution parameter" value="1" min="0"/>
103 </when>
104 <when value="false" />
105 </conditional>
106 <param name="removeGap" type="select" display="radio" label="Remove gap strategy">
107 <option value="">Pairwise deletion of gaps</option>
108 <option value="--remove_gap">Remove all sites with gap</option>
109 </param>
110 <param name="distance" type="select" label="Distance algorithm">
111 <option value="--method=I">BIONJ</option>
112 <option value="--method=B --branch_length=B">TaxAdd BalME</option>
113 <option value="--method=O --branch_length=O">TaxAdd OLSME</option>
114 <option value="--method=N">NJ</option>
115 <option value="--method=U">UNJ</option>
116 </param>
117 <param name="treeRefinement" type="select" display="radio" label="Tree Refinement" help='(NNI) Nearest Neighbor Interchanges,(SPR) Subtree Pruning and Regrafting '>
118 <option value="">None</option>
119 <option value="--nni=O">OLS NNI</option>
120 <option value="--nni=B">BalME NNI</option>
121 <option value="--spr" selected="true">BalME SPR</option>
122 <option value="--nni=B --spr">BalME NNI + SPR</option>
123 </param>
124 <conditional name="bootChoice">
125 <param name="boot" type="select" label="Bootstrap">
126 <option value="false">No</option>
127 <option value="true">Yes</option>
128 </param>
129 <when value="false"/>
130 <when value="true">
131 <param name="replicates" type="integer" value="1000" label="Number of replicates"/>
132 </when>
133 </conditional>
134 </inputs>
135 <outputs>
136 <data name="outputTree" format="nhx" label="${fileout_label}"/>
137 <data name="outputLog" format="txt" label="FastME Information"/>
138 <data name="outputBoostrap" format="nhx" label="FastME Bootstrap trees">
139 <filter>bootChoice['boot'] == "true"</filter>
140 </data>
141 <data name="outputMatrix" format="txt" label="FastME Distance matrix"/>
142 </outputs>
143 <tests>
144 <test>
145 <param name="input" value="phylip" />
146 <param name="modeldna" value="4"/>
147 <param name="gamma" value="false"/>
148 <param name="treeRefinement" value=""/>
149 <param name="distance" value="--method=I"/>
150 <output name="outputTree" file="newick" />
151 </test>
152 <test>
153 <param name="input" value="phylip" />
154 <param name="modeldna" value="T"/>
155 <param name="distance" value="--method=I"/>
156 <param name="treeRefinement" value="--nni=B --spr"/>
157 <param name="fileout_label" value="TreeTn93BionjSpr.nwk" />
158 <output name="outputTree" file="TreeTn93BionjSpr.nwk" />
159 </test>
160 </tests>
161 <help><![CDATA[
162
163 .. class:: infomark
164
165 **FastME** version 2.1.5 http://www.atgc-montpellier.fr/fastme
166
167 .. class:: infomark
168
169 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
170
171 .. class:: infomark
172
173 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
174
175 -----
176
177
178 ############
179 FastME 2.0
180 ############
181
182 -----------
183 Description
184 -----------
185
186 Comprehensive, accurate and fast distance-based phylogeny inference program
187
188 FastME provides distance algorithms to infer phylogenies. It's based on balanced minimum evolution, which is the very principle of NJ.
189
190 FastME included Nearest Neighbor Interchange (NNI) and also Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.
191
192 For further informations, please visit FastME website_
193
194 .. _website: http://www.atgc-montpellier.fr/fastme/usersguide.php
195
196
197 ------------
198 Dependencies
199 ------------
200 FASTME
201 fastme_ 2.1.5 , Conda version
202
203 .. _fastme: https://anaconda.org/bioconda/fastme
204
205
206 ---------------------------------------------------
207
208 ---------------
209 Working example
210 ---------------
211
212 Input files
213 ===========
214
215 **Phylip file**::
216
217
218 4 120
219 Orangutan CCAAACGACA TTTCATATGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTGTCCGGAA
220 Gorilla CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTCTCCGAAA
221 Human CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATAAGA GACAAGTGAG CTCTCCGAAA
222 Chimp CCAAACAACA TTTCATGTGC TGTCATTTCT GAAGATATGA GACAAGTGAG CTCTCCGAAA
223
224 CCAACATATC AGACATATGT GAATTTCAAT TATTGTACGG GCATCCTGGG CTCTCAAAGT
225 CCAAGATATC AGACATTTAT GAATTTCAAT TATTGTACGG GCATCCTGGG CTCTCAAAGT
226 CCAAGATACC AGACATTTGT GAATTTCAAT TATTGTACTG GCATCCTGGG CTCTCAAAGT
227 CCAAGATATC AGACATTTAT GAATTTCAAT TATTGTACTG GCATCCTGGG CTCTCAAAGT
228
229
230
231 Parameters
232 ==========
233
234 ::
235
236 Output name: Newick tree
237 Evolutionary model : TN93
238 Distance method : BIONJ
239
240
241 Output file
242 ===========
243
244 **Newick tree**::
245
246 ((Gorilla:0.005755,Orangutan:0.020680):0.001063,Human:0.006655,Chimp:0.002132);
247
248 -----
249
250 OPTIONS
251 =======
252
253
254 -i file, --input_data=file
255 The input data file contains sequence alignment(s) or a distance matrix(ces).
256
257 -u input_tree_file, --user_tree=input_tree_file
258 FastME may use an existing topology available in the input user tree file which corresponds to the input dataset.
259
260 -o output_tree_file, --output_tree=output_tree_file
261 FastME will write the infered tree into the output tree file.
262
263 -O output_matrix_file, --output_matrix=output_matrix_file
264 Use output matrix file option if you want FastME to write the distances
265 matrix computed from the input alignment in the output matrix file.
266
267 -I output_information_file, --output_info=output_information_file
268 Use this option if you want FastME to write information
269 about its execution in the output information file.
270
271 -B output_bootstrap_trees_file, --output_boot=output_bootstrap_trees_file
272 Use this option if you want FastME to write bootstrap trees
273 in the bootstrap trees file.
274
275 -a, --append
276 Use this option to append results to existing output files (if any).
277 By default output files will be overwritten.
278
279 -m method, --method=method
280 FastME computes a tree using a distance algorithm.
281 You may choose this method from:
282 TaxAdd_(B)alME, TaxAdd_(O)LSME, B(I)ONJ (default),
283 (N)J or (U)NJ.
284
285 -d model, --dna=model
286 Use this option if your input data file contains DNA sequences alignment(s).
287 You may also indicate the evolutionary [model] which can be choosen from:
288 (p)-distance, R(Y) symmetric, (R)Y, (J)C69, (K)2P, F8(1), F8(4) (default), (T)N93, (L)ogDet.
289
290 -p model, --protein=model
291 Use this option if your input data file contains protein sequences alignment(s).
292 You may also indicate the evolutionary [model] which can be choosen from:
293 (p)-distance, (F)81 like, (L)G (default), (W)AG, (J)TT, Day(h)off, (D)CMut, (C)pRev,
294 (M)tREV, (R)tREV, HIV(b), H(I)Vw or FL(U).
295
296 -r, --remove_gap
297 Use this option to completely remove any site which has a gap in
298 any sequence. By default, FastME is doing pairwise deletion of gaps.
299
300 -e, --equilibrium
301 The equilibrium frequencies for DNA are always estimated by counting
302 the occurence of the nucleotides in the input alignment.
303 For amino-acid sequences, the equilibrium frequencies are estimated
304 using the frequencies defined by the substitution model.
305 Use this option if you whish to estimate the amino-acid frequencies
306 by counting their occurence in the input alignment.
307
308 -g alpha, --gamma=alpha
309 Use this option if you wish to have gamma distributed rates across sites.
310 By default, FastME runs with no gamma variation.
311 If running FastME with gamma distributed rates across sites, the [alpha] default value is 1.0.
312 Only helpful when the input data file contains sequences alignment(s).
313
314 -n NNI, --nni=NNI
315 Use this option to do [NNI] tree topology improvement.
316 You may choose the [NNI] type from:
317 NNI_(B)alME (default) or NNI_(O)LS.
318
319 -s, --spr
320 Use this option to do SPR tree topology improvement.
321
322 -w branch, --branch_length=branch
323 Use this option to indicate the branch length to assign to the tree.
324 Only helpful when not improving the tree topology (no NNI nor SPR).
325 You may choose the branch length from:
326 (B)alLS (default), (O)LS or (n)one. (n)one is only available with BIONJ, NJ or UNJ.
327
328 -D datasets, --datasets=datasets
329 Use this option to indicate the number of datasets in your input
330 data file. Default value is 1.
331
332 -b replicates, --bootstrap=replicates
333 Use this option to indicate the number of replicates FastME will
334 do for bootstrapping. Default value is 0.
335 Only helpful when the input data file contains sequences alignment(s).
336
337 -z seed, --seed=seed
338 Use this option to initialize randomization with seed value. Only helpful when bootstrapping.
339
340 -c Use this option if you want FastME only to compute distance matrix.
341 Only helpful when the input data file contains sequences alignment(s).
342
343 -T number_of_threads, --nb_threads=number_of_threads
344 Use this option to set the number of threads to use.
345 Default number of threads is 4.
346
347 -v value, --verbose=value
348 Sets the verbose level to value [0-3]. Default value is 0
349
350 -V, --version
351 Prints the FastME version.
352
353 -h, --help Display this usage.
354
355
356 ]]></help>
357 <citations>
358 <citation type="doi">10.1093/molbev/msv150</citation>
359 <citation type="doi">10.1089/106652702761034136</citation>
360 </citations>
361 </tool>