Mercurial > repos > iuc > hyphy_fel
comparison hyphy_fel.xml @ 9:8389039f7fbc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
author | iuc |
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date | Fri, 27 Mar 2020 13:19:17 -0400 |
parents | 4eba0baf0278 |
children | 2e5ab7526bd4 |
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8:6400b683aced | 9:8389039f7fbc |
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15 --branches '$branches' | 15 --branches '$branches' |
16 --srv '$include_srv' | 16 --srv '$include_srv' |
17 --pvalue '$p_value' | 17 --pvalue '$p_value' |
18 --output '$fel_output' | 18 --output '$fel_output' |
19 > '$fel_log' | 19 > '$fel_log' |
20 ; | |
21 @CATCH_MPIERR@ | |
20 ]]></command> | 22 ]]></command> |
21 <inputs> | 23 <inputs> |
22 <expand macro="inputs"/> | 24 <expand macro="inputs"/> |
23 <expand macro="gencode"/> | 25 <expand macro="gencode"/> |
24 <expand macro="branches"/> | 26 <expand macro="branches"/> |
40 </test> | 42 </test> |
41 </tests> | 43 </tests> |
42 <help><![CDATA[ | 44 <help><![CDATA[ |
43 FEL : Fixed effects likelihood | 45 FEL : Fixed effects likelihood |
44 ============================== | 46 ============================== |
45 | 47 |
46 What question does this method answer? | 48 What question does this method answer? |
47 -------------------------------------- | 49 -------------------------------------- |
48 | 50 |
49 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection? | 51 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection? |
50 | 52 |
51 Recommended Applications | 53 Recommended Applications |
52 ------------------------ | 54 ------------------------ |
53 | 55 |
54 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics | 56 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics |
55 (or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which | 57 (or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which |
56 represent candidate sites subject to strong selective pressures across the entire phylogeny. | 58 represent candidate sites subject to strong selective pressures across the entire phylogeny. |
57 | 59 |
58 FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. | 60 FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. |
59 | 61 |
60 Brief description | 62 Brief description |
61 ----------------- | 63 ----------------- |
65 determine if beta != alpha at a site. The estimates aggregate | 67 determine if beta != alpha at a site. The estimates aggregate |
66 information over all branches, so the signal is derived from pervasive | 68 information over all branches, so the signal is derived from pervasive |
67 diversification or conservation. A subset of branches can be selected | 69 diversification or conservation. A subset of branches can be selected |
68 for testing as well, in which case an additional (nuisance) parameter | 70 for testing as well, in which case an additional (nuisance) parameter |
69 will be inferred -- the non-synonymous rate on branches NOT selected for | 71 will be inferred -- the non-synonymous rate on branches NOT selected for |
70 testing. | 72 testing. |
71 | 73 |
72 | 74 |
73 Input | 75 Input |
74 ----- | 76 ----- |
75 | 77 |
94 Tool options | 96 Tool options |
95 ------------ | 97 ------------ |
96 | 98 |
97 :: | 99 :: |
98 | 100 |
99 --code Which genetic code to use | 101 --code Which genetic code to use |
100 | 102 |
101 --branches Which branches should be tested for selection? | 103 --branches Which branches should be tested for selection? |
102 All [default] : test all branches | 104 All [default] : test all branches |
103 | 105 |
104 Internal : test only internal branches (suitable for | 106 Internal : test only internal branches (suitable for |
105 intra-host pathogen evolution for example, where terminal branches | 107 intra-host pathogen evolution for example, where terminal branches |
106 may contain polymorphism data) | 108 may contain polymorphism data) |
107 | 109 |
108 Leaves: test only terminal (leaf) branches | 110 Leaves: test only terminal (leaf) branches |
109 | 111 |
110 Unlabeled: if the Newick string is labeled using the {} notation, | 112 Unlabeled: if the Newick string is labeled using the {} notation, |
111 test only branches without explicit labels | 113 test only branches without explicit labels |
112 (see http://hyphy.org/tutorials/phylotree/) | 114 (see http://hyphy.org/tutorials/phylotree/) |
113 | 115 |
114 --pvalue The significance level used to determine significance | 116 --pvalue The significance level used to determine significance |
115 | 117 |
116 --srv Include site-to-site synonymous rate variation? | 118 --srv Include site-to-site synonymous rate variation? |
117 Yes [default] or No | 119 Yes [default] or No |
118 | 120 |
119 | 121 |
120 | 122 |
121 | 123 |
122 ]]> | 124 ]]> |
123 | 125 |
124 </help> | 126 </help> |
125 | 127 |
126 <expand macro="citations"> | 128 <expand macro="citations"> |
127 <citation type="doi">10.1093/molbev/msi105</citation> | 129 <citation type="doi">10.1093/molbev/msi105</citation> |
128 </expand> | 130 </expand> |
129 </tool> | 131 </tool> |