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comparison hyphy_prime.xml @ 0:725ef5f6d749 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 13:15:01 -0400
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1 <?xml version="1.0"?>
2 <tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy0">
3 <description>Property Informed Models of Evolution</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' prime_input.fa &&
10 ln -s '$input_nhx' prime_input.nhx &&
11 @HYPHYMPI@ prime
12 --alignment ./prime_input.fa
13 --tree ./prime_input.nhx
14 --code '$gencodeid'
15 --branches '$branches'
16 --pvalue '$p_value'
17 --properties '$prop_set'
18 --output '$prime_output'
19 > '$prime_log'
20 ;
21 @CATCH_MPIERR@
22 ]]></command>
23 <inputs>
24 <expand macro="inputs"/>
25 <expand macro="gencode"/>
26 <expand macro="branches"/>
27 <param name="prop_set" type="select" label="Biochemical properties to use">
28 <option value="Atchley">Atchley</option>
29 <option value="LCAP">LCAP</option>
30 </param>
31 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
32 </inputs>
33 <outputs>
34 <data name="prime_log" format="txt"/>
35 <data name="prime_output" format="hyphy_results.json" />
36 </outputs>
37 <tests>
38 <test>
39 <param name="input_file" ftype="fasta" value="prime-in1.fa"/>
40 <param name="input_nhx" ftype="nhx" value="prime-in1.nhx"/>
41 <param name="branches" value="All"/>
42 <param name="p_value" value="0.1"/>
43 <param name="prop_set" value="Atchley"/>
44 <output name="prime_output" file="prime-out1.json" compare="sim_size"/>
45 </test>
46 </tests>
47 <help><![CDATA[
48 PRIME: Property Informed Model of Evolution
49 ===========================================
50
51 What question does this method answer?
52 --------------------------------------
53
54 Does evolution at specific sites in a coding alignment preserve or alter some biochemical properties?
55
56 Recommended Applications
57 ------------------------
58
59 Identify biochemical evolutionary constraints or changes with site level resolution: e.g. site 23 is
60 evolving to conserve residue polarity, but alter it's volume.
61
62
63 Brief description
64 -----------------
65
66 Most methods of coding sequence analysis do not take direct account of the fact that
67 the rate at which amino-acids are exchanged is different depending on the amino-acids.
68 While this seems obvious (e.g. radical changes should happen slower), there are many technical reasons
69 for why the standard assumption of "one-rate for all residues" holds.
70
71
72 Given a set of N amino-acid properties, fit a site-level model where non-synonymous rates
73 depend on how much a non-synonymous substitution changes the properties
74 of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )-
75 lambda_2 * diff_2 (X,Y) -...). When lambda_k > 0, changes in property k
76 are disfavored and when lambda_k < 0 -- they are promoted. At each site,
77 N+1 tests are performed (one for each property, and an omnibus test).
78
79 Input
80 -----
81
82 1. A *FASTA* sequence alignment.
83 2. A phylogenetic tree in the *Newick* format
84
85 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
86
87
88 Output
89 ------
90
91 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
92
93 A custom visualization module for viewing these results will soon be available at http://vision.hyphy.org/
94
95 Further reading
96 ---------------
97
98 http://hyphy.org/methods/selection-methods/#PRIME
99
100
101 Tool options
102 ------------
103 ::
104
105
106 --code Which genetic code to use
107
108 --branches Which branches should be tested for selection?
109 All [default] : test all branches
110
111 Internal : test only internal branches (suitable for
112 intra-host pathogen evolution for example, where terminal branches
113 may contain polymorphism data)
114
115 Leaves: test only terminal (leaf) branches
116
117 Unlabeled: if the Newick string is labeled using the {} notation,
118 test only branches without explicit labels
119 (see http://hyphy.org/tutorials/phylotree/)
120
121 --pvalue The significance level used to determine significance
122
123 --properties Which property set to use
124 Atchley : Use the five properties derived from a factor analysis of 500 amino-acid properties [Table 2 in PNAS (2005) 102(18) 6395-6400 doi: 10.1073/pnas.0408677102]
125 LCAP: Use the five properties defined in the Conant and Stadler LCAP model [Mol Biol Evol (2009) 26 (5): 1155-1161. doi: 10.1093/molbev/msp031]
126
127
128 ]]></help>
129 <!--<expand macro="citations">
130 <citation type="doi">10.1371/journal.pgen.1002764</citation>
131 </expand>-->
132 </tool>