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comparison fastMe_main/fastme.xml @ 0:3ef62be50f9d draft

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author gandres
date Wed, 01 Jul 2015 10:43:05 -0400
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1 <tool id="sniplay_fastme" name="FastME" version="1.0.2">
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 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
13 <version_command>
14 <!--
15 tool_binary -v
16 -->
17 </version_command>
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 > $fileout_log
35 </command>
36
37 <!-- [REQUIRED] Input files and tool parameters -->
38 <inputs>
39 <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
40 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
41 <param name="model" type="select" label="Evolutionary model" >
42 <option value="p">p-distance</option>
43 <option value="Y">RY symetric</option>
44 <option value="R">RY</option>
45 <option value="J">JC69</option>
46 <option value="K">K2P</option>
47 <option value="1">F81</option>
48 <option value="4" selected="true">F84</option>
49 <option value="T">TN93</option>
50 <option value="L">LogDet</option>
51 </param>
52 <param name="distance" type="select" label="Distance methode" >
53 <option value="B">TaxAdd_BalME</option>
54 <option value="O">TaxAdd_OLSME</option>
55 <option value="I" selected="true">BIONJ</option>
56 <option value="N">NJ</option>
57 <option value="U">UNJ</option>
58 <option value="NNI_B">NNI_BalME</option>
59 <option value="NNI_O">NNI_OLS</option>
60 <option value="SPR">SPR</option>
61 </param>
62 </inputs>
63
64 <!-- [REQUIRED] Output files -->
65 <outputs>
66 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
67 <data name="fileout" type="data" format="txt" label="${fileout_label}" />
68 </outputs>
69
70 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
71 <stdio>
72 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
73 <exit_code range="1:" level="fatal" />
74 </stdio>
75
76 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
77 <tests>
78 <!-- [HELP] Test files have to be in the ~/test-data directory -->
79
80 <test>
81 <param name="filein" value="phylip" />
82 <param name="model" value="4"/>
83 <param name="distance" value="I"/>
84 <output name="fileout" file="newick" />
85 <output name="fileout_log" file="newick.log" />
86 </test>
87
88 <!-- [HELP] Multiple tests can be defined with different parameters -->
89 <!--
90 <test>
91 </test>
92 -->
93 </tests>
94
95 <!-- [OPTIONAL] Help displayed in Galaxy -->
96 <help>
97
98 .. class:: infomark
99
100 **Authors**
101
102 | Richard Desper and Olivier Gascuel,
103 | Journal of Computational Biology 19(5), 687-705, 2002.
104 | Molecular Biology and Evolution 21(3), 587-598, 2004.
105 | Please cite these papers if you use this software in your publications.
106
107
108 .. class:: infomark
109
110 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
111
112 .. class:: infomark
113
114 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
115
116 ---------------------------------------------------
117
118
119 ======
120 FastMe
121 ======
122
123 -----------
124 Description
125 -----------
126
127 FastME - A distance based phylogeny reconstruction algorithm.
128
129 FastME showed better topological accuracy than NJ,
130 BIONJ, WEIGHBOR and FITCH, in all evolutionary
131 conditions we tested, which include large range
132 deviations from molecular clock and substitution rates.
133
134
135
136 -----------------
137 Workflow position
138 -----------------
139
140 **Upstream tools**
141
142 =========== ========================== =======
143 Name output file(s) format
144 =========== ========================== =======
145 Readseq phylip conversion phylip
146 =========== ========================== =======
147
148
149 **Downstream tools**
150
151 =========== ========================== =======
152 Name output file(s) format
153 =========== ========================== =======
154 Rooting out tree Newick
155 =========== ========================== =======
156
157
158 ----------
159 Input file
160 ----------
161
162 Phylip file
163 Phylip file with sequence alignments
164
165
166 ----------
167 Parameters
168 ----------
169
170 Output name
171 Output base name for the ouput files
172
173 Evolutionary model
174 Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet.
175
176 Distance methode
177 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
178
179 ------------
180 Output files
181 ------------
182
183 Output_name
184 Resulting tree at Newick format
185
186 Output_name.log
187 Log file
188
189 ------------
190 Dependencies
191 ------------
192 FastME
193 http://www.atgc-montpellier.fr/fastme
194
195
196
197 ---------------------------------------------------
198
199 ---------------
200 Working example
201 ---------------
202
203 Input files
204 ===========
205
206 Philip file
207 -----------
208
209 ::
210
211 168 5125
212 IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
213 KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT
214
215 Parameters
216 ==========
217
218 Output name -> Newick tree
219
220 Evolutionary model -> F84
221
222 Distance methode -> BIONJ
223
224 Output files
225 ============
226
227 Newick tree
228 -----------
229
230 ::
231
232 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
233
234
235 </help>
236
237 </tool>