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comparison fastme.xml @ 2:40200a22dba3 draft

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date Fri, 11 Dec 2015 09:16:34 -0500
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1 <tool id="sniplay_fastme" name="Fassqa" version="1.1.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Calculate distance tree for an alignment file</description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="2.1.4">fastme</requirement>
10 </requirements>
11
12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <stdio>
14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
15 <exit_code range="1:" level="fatal" />
16 </stdio>
17
18
19 <!-- [REQUIRED] The command to execute -->
20 <command>
21 fastme --input_data=$input_data --dna=$model --output_tree=$fileout
22 #if str( $distance ) == "SPR":
23 --spr
24 #elif str( $distance )[:3] == "NNI" :
25 #if str( $distance ) == "NNI_B" :
26 --nni=B
27 #else :
28 --nni=O
29 #end if
30
31 #else :
32 --method=$distance
33 #end if
34 > $fileout_log
35 </command>
36
37
38
39 <!-- [REQUIRED] Input files and tool parameters -->
40 <inputs>
41 <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
42 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
43 <param name="model" type="select" label="Evolutionary model" >
44 <option value="p">p-distance</option>
45 <option value="Y">RY symetric</option>
46 <option value="R">RY</option>
47 <option value="J">JC69</option>
48 <option value="K">K2P</option>
49 <option value="1">F81</option>
50 <option value="4" selected="true">F84</option>
51 <option value="T">TN93</option>
52 <option value="L">LogDet</option>
53 </param>
54 <param name="distance" type="select" label="Distance methode" >
55 <option value="B">TaxAdd_BalME</option>
56 <option value="O">TaxAdd_OLSME</option>
57 <option value="I" selected="true">BIONJ</option>
58 <option value="N">NJ</option>
59 <option value="U">UNJ</option>
60 <option value="NNI_B">NNI_BalME</option>
61 <option value="NNI_O">NNI_OLS</option>
62 <option value="SPR">SPR</option>
63 </param>
64 </inputs>
65
66 <!-- [REQUIRED] Output files -->
67 <outputs>
68 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
69 <data name="fileout" type="data" format="txt" label="${fileout_label}" />
70 </outputs>
71
72 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
73 <tests>
74 <!-- [HELP] Test files have to be in the ~/test-data directory -->
75
76 <test>
77 <param name="input_data" value="phylip" />
78 <param name="model" value="4"/>
79 <param name="distance" value="I"/>
80 <output name="fileout" file="newick" />
81 </test>
82
83 <!-- [HELP] Multiple tests can be defined with different parameters -->
84 <!--
85 <test>
86 </test>
87 -->
88 </tests>
89
90 <!-- [OPTIONAL] Help displayed in Galaxy -->
91 <help>
92
93 .. class:: infomark
94
95 **Authors**
96
97 | Richard Desper and Olivier Gascuel,
98 | Journal of Computational Biology 19(5), 687-705, 2002.
99 | Molecular Biology and Evolution 21(3), 587-598, 2004.
100 | Please cite these papers if you use this software in your publications.
101
102
103 .. class:: infomark
104
105 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
106
107 .. class:: infomark
108
109 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
110
111 ---------------------------------------------------
112
113
114 ======
115 FastMe
116 ======
117
118 -----------
119 Description
120 -----------
121
122
123 FastME - A distance based phylogeny reconstruction algorithm.
124
125 FastME showed better topological accuracy than NJ,
126 BIONJ, WEIGHBOR and FITCH, in all evolutionary
127 conditions we tested, which include large range
128 deviations from molecular clock and substitution rates.
129
130
131
132 -----------------
133 Workflow position
134 -----------------
135
136 **Upstream tools**
137
138 =========== ========================== =======
139 Name output file(s) format
140 =========== ========================== =======
141 Readseq phylip conversion phylip
142 =========== ========================== =======
143
144
145 **Downstream tools**
146
147 =========== ========================== =======
148 Name output file(s) format
149 =========== ========================== =======
150 Rooting out tree Newick
151 =========== ========================== =======
152
153
154 ----------
155 Input file
156 ----------
157
158 Phylip file
159 Phylip file with sequence alignments
160
161
162 ----------
163 Parameters
164 ----------
165
166 Output name
167 Output base name for the ouput files
168
169 Evolutionary model
170 Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet.
171
172 Distance methode
173 FastME computes a tree using a distance algorithm. You may choose this method/topologie from: TaxAdd_BalME, TaxAdd_OLSME, BIONJ (default), NJ, UNJ, NNI_BalME, NNI_OLS or SPR
174
175 ------------
176 Output files
177 ------------
178
179 Output_name
180 Resulting tree at Newick format
181
182 Output_name.log
183 Log file
184
185 ------------
186 Dependencies
187 ------------
188 FastME
189 http://www.atgc-montpellier.fr/fastme
190
191
192
193 ---------------------------------------------------
194
195 ---------------
196 Working example
197 ---------------
198
199 Input files
200 ===========
201
202 Philip file
203 -----------
204
205 ::
206
207 168 5125
208 IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
209 KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT
210
211 Parameters
212 ==========
213
214 Output name -> Newick tree
215
216 Evolutionary model -> F84
217
218 Distance methode -> BIONJ
219
220 Output files
221 ============
222
223 Newick tree
224 -----------
225
226 ::
227
228 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
229
230
231 </help>
232
233 <citations>
234 <!-- [HELP] As DOI or BibTex entry -->
235 <citation type="bibtex">
236 @article{Lefort30062015,
237 author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier},
238 title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program},
239 year = {2015},
240 doi = {10.1093/molbev/msv150},
241 abstract ={FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, 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. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).},
242 URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract},
243 eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html},
244 journal = {Molecular Biology and Evolution}
245 }
246
247 </citation>
248
249 </citations>
250
251
252 </tool>