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comparison hyphy_meme.xml @ 8:3d1f153e2aa1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
author iuc
date Fri, 27 Mar 2020 13:18:02 -0400
parents 74b590fdc6a0
children 5b380f4dbf1c
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7:74b590fdc6a0 8:3d1f153e2aa1
14 --code '$gencodeid' 14 --code '$gencodeid'
15 --branches '$branches' 15 --branches '$branches'
16 --pvalue '$p_value' 16 --pvalue '$p_value'
17 --output '$meme_output' 17 --output '$meme_output'
18 > '$meme_log' 18 > '$meme_log'
19 ;
20 @CATCH_MPIERR@
19 ]]></command> 21 ]]></command>
20 <inputs> 22 <inputs>
21 <expand macro="inputs"/> 23 <expand macro="inputs"/>
22 <expand macro="gencode"/> 24 <expand macro="gencode"/>
23 <expand macro="branches"/> 25 <expand macro="branches"/>
37 </test> 39 </test>
38 </tests> 40 </tests>
39 <help><![CDATA[ 41 <help><![CDATA[
40 MEME: Mixed Effects Model of Evolution 42 MEME: Mixed Effects Model of Evolution
41 ====================================== 43 ======================================
42 44
43 What question does this method answer? 45 What question does this method answer?
44 -------------------------------------- 46 --------------------------------------
45 47
46 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a 48 Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
47 single lineage or subset of lineages, diversifying selection? 49 single lineage or subset of lineages, diversifying selection?
48 50
49 Recommended Applications 51 Recommended Applications
50 ------------------------ 52 ------------------------
51 53
52 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics 54 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
53 (or balancing selection), including adaptive immune escape by viruses. 55 (or balancing selection), including adaptive immune escape by viruses.
54 MEME is ideally suited to identify sites under positive selection which 56 MEME is ideally suited to identify sites under positive selection which
55 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny. 57 represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.
56 58
57 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection. 59 MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
58 MEME is therefore our recommended method if maximum power is desired. 60 MEME is therefore our recommended method if maximum power is desired.
59 61
60 62
61 Brief description 63 Brief description
62 ----------------- 64 -----------------
63 65
97 Tool options 99 Tool options
98 ------------ 100 ------------
99 :: 101 ::
100 102
101 103
102 --code Which genetic code to use 104 --code Which genetic code to use
103 105
104 --branches Which branches should be tested for selection? 106 --branches Which branches should be tested for selection?
105 All [default] : test all branches 107 All [default] : test all branches
106 108
107 Internal : test only internal branches (suitable for 109 Internal : test only internal branches (suitable for
108 intra-host pathogen evolution for example, where terminal branches 110 intra-host pathogen evolution for example, where terminal branches
109 may contain polymorphism data) 111 may contain polymorphism data)
110 112
111 Leaves: test only terminal (leaf) branches 113 Leaves: test only terminal (leaf) branches
112 114
113 Unlabeled: if the Newick string is labeled using the {} notation, 115 Unlabeled: if the Newick string is labeled using the {} notation,
114 test only branches without explicit labels 116 test only branches without explicit labels
115 (see http://hyphy.org/tutorials/phylotree/) 117 (see http://hyphy.org/tutorials/phylotree/)
116 118
117 --pvalue The significance level used to determine significance 119 --pvalue The significance level used to determine significance
118 120
119 121
120 ]]></help> 122 ]]></help>
121 <expand macro="citations"> 123 <expand macro="citations">
122 <citation type="doi">10.1371/journal.pgen.1002764</citation> 124 <citation type="doi">10.1371/journal.pgen.1002764</citation>
123 </expand> 125 </expand>