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comparison fastMe_main/fastme.xml @ 1:6362669c440a draft

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author gandres
date Fri, 02 Oct 2015 10:55:52 -0400
parents 3ef62be50f9d
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0:3ef62be50f9d 1:6362669c440a
1 <tool id="sniplay_fastme" name="FastME" version="1.0.2"> 1 <tool id="sniplay_fastme" name="FastME" version="1.1.0">
2 2
3 <!-- [REQUIRED] Tool description displayed after the tool name --> 3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Calculate distance tree for an alignment file</description> 4 <description> Calculate distance tree for an alignment file</description>
5 5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements> 7 <requirements>
8 <requirement type="binary">perl</requirement> 8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="2.1.4">fastme</requirement> 9 <requirement type="package" version="2.1.4">fastme
10 </requirement>
10 </requirements> 11 </requirements>
11 12
12 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> 13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <version_command> 14 <stdio>
14 <!-- 15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
15 tool_binary -v 16 <exit_code range="1:" level="fatal" />
16 --> 17 </stdio>
17 </version_command> 18
18 19
19 <!-- [REQUIRED] The command to execute --> 20 <!-- [REQUIRED] The command to execute -->
20 <command> 21 <command>
21 fastme --input_data=$input_data --dna=$model --output_tree=$fileout 22 fastme --input_data=$input_data --dna=$model --output_tree=$fileout
22 #if str( $distance ) == "SPR": 23 #if str( $distance ) == "SPR":
32 --method=$distance 33 --method=$distance
33 #end if 34 #end if
34 > $fileout_log 35 > $fileout_log
35 </command> 36 </command>
36 37
38
39
37 <!-- [REQUIRED] Input files and tool parameters --> 40 <!-- [REQUIRED] Input files and tool parameters -->
38 <inputs> 41 <inputs>
39 <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" /> 42 <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
40 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" /> 43 <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
44 <param name="fileout_label2" type="text" value="Unused" label="none" help="Output name for files" />
41 <param name="model" type="select" label="Evolutionary model" > 45 <param name="model" type="select" label="Evolutionary model" >
42 <option value="p">p-distance</option> 46 <option value="p">p-distance</option>
43 <option value="Y">RY symetric</option> 47 <option value="Y">RY symetric</option>
44 <option value="R">RY</option> 48 <option value="R">RY</option>
45 <option value="J">JC69</option> 49 <option value="J">JC69</option>
65 <outputs> 69 <outputs>
66 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> 70 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
67 <data name="fileout" type="data" format="txt" label="${fileout_label}" /> 71 <data name="fileout" type="data" format="txt" label="${fileout_label}" />
68 </outputs> 72 </outputs>
69 73
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 --> 74 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
77 <tests> 75 <tests>
78 <!-- [HELP] Test files have to be in the ~/test-data directory --> 76 <!-- [HELP] Test files have to be in the ~/test-data directory -->
79 77
80 <test> 78 <test>
122 120
123 ----------- 121 -----------
124 Description 122 Description
125 ----------- 123 -----------
126 124
125
127 FastME - A distance based phylogeny reconstruction algorithm. 126 FastME - A distance based phylogeny reconstruction algorithm.
128 127
129 FastME showed better topological accuracy than NJ, 128 FastME showed better topological accuracy than NJ,
130 BIONJ, WEIGHBOR and FITCH, in all evolutionary 129 BIONJ, WEIGHBOR and FITCH, in all evolutionary
131 conditions we tested, which include large range 130 conditions we tested, which include large range
232 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... 231 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
233 232
234 233
235 </help> 234 </help>
236 235
236 <citations>
237 <!-- [HELP] As DOI or BibTex entry -->
238 <citation type="bibtex">
239 @article{Lefort30062015,
240 author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier},
241 title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program},
242 year = {2015},
243 doi = {10.1093/molbev/msv150},
244 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/).},
245 URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract},
246 eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html},
247 journal = {Molecular Biology and Evolution}
248 }
249
250 </citation>
251
252 </citations>
253
254
237 </tool> 255 </tool>