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comparison hyphy_absrel.xml @ 9:fef84cff2eb7 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 16:20:29 +0000
parents 756a2d3b632b
children f293295d5233
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8:9e8a2f331ee5 9:fef84cff2eb7
15 --branches '$branches' 15 --branches '$branches'
16 --output '$absrel_output' 16 --output '$absrel_output'
17 #if $log: 17 #if $log:
18 > '$absrel_log' 18 > '$absrel_log'
19 #end if 19 #end if
20 ;
21 @CATCH_MPIERR@
20 ]]></command> 22 ]]></command>
21 <inputs> 23 <inputs>
22 <expand macro="inputs"/> 24 <expand macro="inputs"/>
23 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/> 25 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
24 <expand macro="gencode"/> 26 <expand macro="gencode"/>
37 <param name="log" value="false"/> 39 <param name="log" value="false"/>
38 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> 40 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
39 </test> 41 </test>
40 </tests> 42 </tests>
41 <help><![CDATA[ 43 <help><![CDATA[
42 44
43 aBSREL : Adaptive Branch-Site Random Effects Likelihood 45 aBSREL : Adaptive Branch-Site Random 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 Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny? 51 Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?
50 52
51 Recommended Applications 53 Recommended Applications
52 ------------------------ 54 ------------------------
53 55
54 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences). 56 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
55 2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) 57 2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences)
56 58
57 Brief description 59 Brief description
58 ----------------- 60 -----------------
59 61
60 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive 62 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive
75 Output 77 Output
76 ------ 78 ------
77 79
78 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). 80 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
79 81
80 For each tested branch the analysis will infer the appropriate number of selective regimes, 82 For each tested branch the analysis will infer the appropriate number of selective regimes,
81 and whether or not there is statistical evidence of positive selection on that branch. 83 and whether or not there is statistical evidence of positive selection on that branch.
82 84
83 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example) 85 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)
84 86
85 Further reading 87 Further reading
91 Tool options 93 Tool options
92 ------------ 94 ------------
93 :: 95 ::
94 96
95 97
96 --code Which genetic code to use 98 --code Which genetic code to use
97 99
98 --branches Which branches should be tested for selection? 100 --branches Which branches should be tested for selection?
99 All [default] : test all branches 101 All [default] : test all branches
100 102
101 Internal : test only internal branches (suitable for 103 Internal : test only internal branches (suitable for
102 intra-host pathogen evolution for example, where terminal branches 104 intra-host pathogen evolution for example, where terminal branches
103 may contain polymorphism data) 105 may contain polymorphism data)
104 106
105 Leaves: test only terminal (leaf) branches 107 Leaves: test only terminal (leaf) branches
106 108
107 Unlabeled: if the Newick string is labeled using the {} notation, 109 Unlabeled: if the Newick string is labeled using the {} notation,
108 test only branches without explicit labels 110 test only branches without explicit labels
109 (see http://hyphy.org/tutorials/phylotree/) 111 (see http://hyphy.org/tutorials/phylotree/)
110 112
111 113
112 114
113 ]]></help> 115 ]]></help>
114 <expand macro="citations"> 116 <expand macro="citations">
115 <citation type="doi">10.1093/molbev/msv022</citation> 117 <citation type="doi">10.1093/molbev/msv022</citation>
116 </expand> 118 </expand>