Mercurial > repos > iuc > phyml

annotate phyml.xml @ 2:2bf47d57ebb5 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 61b727022bd1b24a8843830a9c5f34ef66835694"
author iuc
date Mon, 22 Jun 2020 18:37:56 -0400
parents 034f76ead49a
children 7157a5b34a68
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
2bf47d57ebb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
parents: 1
diff changeset
1 <tool id="phyml" name="PhyML" version="@VERSION@">
2bf47d57ebb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
parents: 1
diff changeset
2 <description>Phylogeny software based on the maximum-likelihood method.</description>
2bf47d57ebb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
parents: 1
diff changeset
3 <macros>
2bf47d57ebb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
parents: 1
diff changeset
4 <token name="@VERSION@">3.3.20190909</token>
2bf47d57ebb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
parents: 1
diff changeset
5 </macros>
1
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
6 <requirements>
2
2bf47d57ebb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
parents: 1
diff changeset
7 <requirement type="package" version="@VERSION@">phyml</requirement>
1
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
8 </requirements>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
9 <version_command>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
10 <![CDATA[ phyml --version ]]>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
11 </version_command>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
12 <command detect_errors="default">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
13 <![CDATA[
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
14 ##PhyML outputs are based on input path and we need to create outputs in working_dir.
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
15 ln -sf '$input' '${input.name}' &&
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
16 #if $userInputTree:
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
17 ln -sf '${$userInputTree}' '${$userInputTree.name}' &&
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
18 #end if
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
19
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
20 phyml --input '${input.name}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
21 '${phylip_format}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
22 --datatype '${seq.type_of_seq}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
23 --multiple '${nb_data_set}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
24
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
25 #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']):
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
26 --bootstrap '${support_condition.branchSupport}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
27 #else:
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
28 --bootstrap '${support_condition.branchSupport.replicate}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
29 #end if
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
30
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
31 #if $seq.type_of_seq == "nt":
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
32 -t '${seq.tstv}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
33 #end if
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
34
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
35 --model '${seq.model}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
36 -f '${equi_freq}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
37 --pinv '${prop_invar}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
38
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
39 --nclasses '${nbSubstCat}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
40
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
41 #if (str($nbSubstCat) != "1"):
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
42 --alpha '${gamma}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
43 #end if
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
44
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
45 --search '${move}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
46 -o '${optimisationTopology}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
47
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
48 #if $userInputTree:
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
49 --inputtree '${$userInputTree.name}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
50 #end if
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
51
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
52 #if $numStartSeed != "0":
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
53 --r_seed '${numStartSeed}'
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
54 #end if
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
55
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
56 --no_memory_check > '${output_stdout}' &&
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
57 grep 'failed' '${output_stdout}' >&2;
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
58 ]]>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
59 </command>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
60 <inputs>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
61 <param name="input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
62 <param name="phylip_format" type="select" label="Changes interleaved format">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
63 <option value="">Interleaved</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
64 <option value="--sequential">Sequential</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
65 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
66 <param name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
67 <conditional name="seq">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
68 <param name="type_of_seq" type="select" label="Data type">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
69 <option value="nt">Nucleic acids</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
70 <option value="aa">Amino acids</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
71 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
72 <when value="nt">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
73 <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" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
74 <param name="model" type="select" label="Substitution model">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
75 <option value="HKY85">HKY85</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
76 <option value="JC69">JC69</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
77 <option value="K80">K80</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
78 <option value="F81">F81</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
79 <option value="F84">F84</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
80 <option value="TN93">TN93</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
81 <option value="GTR">GTR</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
82 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
83 </when>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
84 <when value="aa">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
85 <param name="model" type="select" label="Evolution model">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
86 <option value="LG">LG</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
87 <option value="WAG">WAG</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
88 <option value="JTT">JTT</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
89 <option value="MtREV">MtREV</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
90 <option value="Dayhoff">Dayhoff</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
91 <option value="DCMut">DCMut</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
92 <option value="RtREV">RtREV</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
93 <option value="CpREV">CpREV</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
94 <option value="VT">VT</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
95 <option value="Blosum62">Blosum62</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
96 <option value="MtMam">MtMam</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
97 <option value="MtArt">MtArt</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
98 <option value="HIVw">HIVw</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
99 <option value="HIVb">HIVb</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
100 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
101 </when>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
102 </conditional>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
103 <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"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
104 <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.">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
105 <option value="m">ML/Model</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
106 <option value="e">Empirical</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
107 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
108 <param name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
109 <param name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
110 <param name="move" type="select" label="Tree topology search">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
111 <option value="NNI">NNI (Nearest Neighbor Interchange)</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
112 <option value="SPR">SPR (Subtree Pruning and Regraphing)</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
113 <option value="BEST">Best of NNI and SPR</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
114 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
115 <param name="optimisationTopology" type="select" label="Optimise topology">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
116 <option value="tlr">Tree topology, Branch length, Rate parameter</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
117 <option value="tl">Tree topology, Branch length</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
118 <option value="l">Branch length</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
119 <option value="r">Rate parameter</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
120 <option value="n">No parameter is optimized</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
121 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
122 <conditional name="support_condition">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
123 <param name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
124 <option value="0">No bootstrap</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
125 <option value="1">Bootstrap</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
126 <option value="-1">likelihood aLRT statistics</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
127 <option value="-2">likelihood Chi2-based</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
128 <option value="-4" selected='true'>SH-like</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
129 <option value="-5">Approximate Bayes branch supports</option>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
130 </param>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
131 <when value="0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
132 <when value="-1"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
133 <when value="-2"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
134 <when value="-4"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
135 <when value="-5"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
136 <when value="1">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
137 <param name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
138 </when>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
139 </conditional>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
140 <param name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
141 <param name="userInputTree" optional="True" type="data" format="nhx" label="Tree file" help="newick format"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
142 </inputs>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
143 <outputs>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
144 <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
145 <data name="output_stats" format="txt" label="PhyML Statistic: ${input.name}.stats.txt" from_work_dir="*_phyml_stats.txt"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
146 <data name="output_stdout" format="txt" label="PhyML Stdout: ${input.name}"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
147 </outputs>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
148 <tests>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
149 <test>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
150 <param name="input" value="phylip" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
151 <param name="prop_invar" value="0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
152 <param name="type_of_seq" value="nt" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
153 <param name="numStartSeed" value="1458308600" />
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
154 <output name="output_tree">
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
155 <assert_contents>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
156 <has_text text="Rhes_cDNA:0.0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
157 <has_text text="Baboon:0.0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
158 <has_text text="Orangutan:0.0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
159 <has_text text="Gibbon:0.0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
160 <has_text text="Human:0.0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
161 <has_text text="Chimp:0.0"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
162 </assert_contents>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
163 </output>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
164 <output name="output_stats" file="phylip_phyml_stats.txt" lines_diff="4"/>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
165 </test>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
166 </tests>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
167 <help>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
168 <![CDATA[
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
169 .. class:: infomark
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
170
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
171 #########
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
172 PhyML 3.3
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
173 #########
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
174
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
175 A simple, fast, and accurate algorithm to estimate
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
176 large phylogenies by maximum likelihood''
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
177
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
178 ==========
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
179 Overview:
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
180 ==========
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
181
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
182 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.
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
183
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
184 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.
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
185
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
186 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.
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
187
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
188 -----
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
189
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
190
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
191 For further informations, please visite the PhyML_ website.
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
192
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
193 .. _PhyML: http://www.atgc-montpellier.fr/phyml/
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
194
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
195 Please cite this paper if you use this software in your publications.
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
196
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
197
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
198 ]]>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
199 </help>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
200 <citations>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
201 <citation type="doi">10.1093/sysbio/syq010</citation>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
202 </citations>
034f76ead49a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit 7262445f852345ec93762ff94642507a2b63f0cd"
iuc
parents: 0
diff changeset
203 </tool>