Mercurial > repos > iuc > phyml

annotate phyml.xml @ 0:850e213bee26 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
author iuc
date Tue, 28 May 2019 13:53:56 -0400
parents
children 034f76ead49a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
1 <tool id="phyml" name="PhyML" version="3.3.20190321">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
2 <description>Phylogeny software based on the maximum-likelihood</description>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
3 <requirements>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
4 <requirement type="package" version="3.3.20190321">phyml</requirement>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
5 </requirements>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
6 <version_command>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
7 <![CDATA[ phyml --version ]]>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
8 </version_command>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
9 <command detect_errors="default">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
10 <![CDATA[
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
11 ##PhyML outputs are based on input path and we need to create outputs in working_dir.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
12 ln -sf '$input' '${input.name}' &&
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
13 #if $userInputTree:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
14 ln -sf '${$userInputTree}' '${$userInputTree.name}' &&
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
15 #end if
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
16
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
17 phyml --input '${input.name}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
18 '${phylip_format}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
19 --datatype '${seq.type_of_seq}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
20 --multiple '${nb_data_set}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
21
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
22 #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']):
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
23 --bootstrap '${support_condition.branchSupport}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
24 #else:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
25 --bootstrap '${support_condition.branchSupport.replicate}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
26 #end if
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
27
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
28 #if $seq.type_of_seq == "nt":
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
29 -t '${seq.tstv}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
30 #end if
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
31
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
32 --model '${seq.model}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
33 -f '${equi_freq}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
34 --pinv '${prop_invar}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
35
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
36 --nclasses '${nbSubstCat}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
37
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
38 #if (str($nbSubstCat) != "1"):
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
39 --alpha '${gamma}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
40 #end if
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
41
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
42 --search '${move}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
43 -o '${optimisationTopology}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
44
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
45 #if $userInputTree:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
46 --inputtree '${$userInputTree.name}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
47 #end if
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
48
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
49 #if $numStartSeed != "0":
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
50 --r_seed '${numStartSeed}'
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
51 #end if
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
52
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
53 --no_memory_check > '${output_stdout}' &&
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
54 grep 'failed' '${output_stdout}' >&2;
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
55 ]]>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
56 </command>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
57 <inputs>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
58 <param name="input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
59 <param name="phylip_format" type="select" label="Changes interleaved format">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
60 <option value="">Interleaved</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
61 <option value="--sequential">Sequential</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
62 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
63 <param name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
64 <conditional name="seq">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
65 <param name="type_of_seq" type="select" label="Data type">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
66 <option value="nt">Nucleic acids</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
67 <option value="aa">Amino acids</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
68 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
69 <when value="nt">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
70 <param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Must be a positive integer, 'e' if you want PhyML to estimate it" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
71 <param name="model" type="select" label="Substitution model">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
72 <option value="HKY85">HKY85</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
73 <option value="JC69">JC69</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
74 <option value="K80">K80</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
75 <option value="F81">F81</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
76 <option value="F84">F84</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
77 <option value="TN93">TN93</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
78 <option value="GTR">GTR</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
79 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
80 </when>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
81 <when value="aa">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
82 <param name="model" type="select" label="Evolution model">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
83 <option value="LG">LG</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
84 <option value="WAG">WAG</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
85 <option value="JTT">JTT</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
86 <option value="MtREV">MtREV</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
87 <option value="Dayhoff">Dayhoff</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
88 <option value="DCMut">DCMut</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
89 <option value="RtREV">RtREV</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
90 <option value="CpREV">CpREV</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
91 <option value="VT">VT</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
92 <option value="Blosum62">Blosum62</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
93 <option value="MtMam">MtMam</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
94 <option value="MtArt">MtArt</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
95 <option value="HIVw">HIVw</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
96 <option value="HIVb">HIVb</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
97 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
98 </when>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
99 </conditional>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
100 <param name="prop_invar" type="text" value="e" label="Proportion of invariant sites" help="Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
101 <param name="equi_freq" type="select" label="Equilibrium frequencies" help="Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model: frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
102 <option value="m">ML/Model</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
103 <option value="e">Empirical</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
104 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
105 <param name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
106 <param name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
107 <param name="move" type="select" label="Tree topology search">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
108 <option value="NNI">NNI (Nearest Neighbor Interchange)</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
109 <option value="SPR">SPR (Subtree Pruning and Regraphing)</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
110 <option value="BEST">Best of NNI and SPR</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
111 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
112 <param name="optimisationTopology" type="select" label="Optimise topology">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
113 <option value="tlr">Tree topology, Branch length, Rate parameter</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
114 <option value="tl">Tree topology, Branch length</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
115 <option value="l">Branch length</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
116 <option value="r">Rate parameter</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
117 <option value="n">No parameter is optimized</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
118 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
119 <conditional name="support_condition">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
120 <param name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
121 <option value="0">No bootstrap</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
122 <option value="1">Bootstrap</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
123 <option value="-1">likelihood aLRT statistics</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
124 <option value="-2">likelihood Chi2-based</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
125 <option value="-4" selected='true'>SH-like</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
126 <option value="-5">Approximate Bayes branch supports</option>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
127 </param>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
128 <when value="0"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
129 <when value="-1"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
130 <when value="-2"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
131 <when value="-4"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
132 <when value="-5"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
133 <when value="1">
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
134 <param name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
135 </when>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
136 </conditional>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
137 <param name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
138 <param name="userInputTree" optional="True" type="data" format="nhx" label="Tree file" help="newick format"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
139 </inputs>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
140 <outputs>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
141 <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
142 <data name="output_stats" format="txt" label="PhyML Statistic: ${input.name}.stats.txt" from_work_dir="*_phyml_stats.txt"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
143 <data name="output_stdout" format="txt" label="PhyML Stdout: ${input.name}"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
144 </outputs>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
145 <tests>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
146 <test>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
147 <param name="input" value="phylip" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
148 <param name="prop_invar" value="0"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
149 <param name="type_of_seq" value="nt" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
150 <param name="numStartSeed" value="1458308600" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
151 <output name="output_tree" file="phylip_phyml_tree.txt" />
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
152 <output name="output_stats" file="phylip_phyml_stats.txt" lines_diff="4"/>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
153 </test>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
154 </tests>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
155 <help>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
156 <![CDATA[
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
157 .. class:: infomark
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
158
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
159 -----
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
160
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
161 #########
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
162 PhyML 3.3
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
163 #########
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
164
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
165 A simple, fast, and accurate algorithm to estimate
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
166 large phylogenies by maximum likelihood''
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
167
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
168 ==========
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
169 Overview:
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
170 ==========
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
171
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
172 PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
173
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
174 We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
175
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
176 It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
177
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
178 -----
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
179
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
180
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
181 For further informations, please visite the PhyML_ website.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
182
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
183 .. _PhyML: http://www.atgc-montpellier.fr/phyml/
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
184
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
185 Please cite this paper if you use this software in your publications.
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
186
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
187
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
188 ]]>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
189 </help>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
190 <citations>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
191 <citation type="doi">10.1093/sysbio/syq010</citation>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
192 </citations>
850e213bee26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 0e9f19277b1bdc8f2a65e605ded44f1a35cd2ea6
iuc
parents:
diff changeset
193 </tool>