Mercurial > repos > iuc > hyphy_prime

annotate hyphy_prime.xml @ 23:840b5fec0de9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
author iuc
date Sat, 27 Nov 2021 11:34:27 +0000
parents b044a346c00d
children f207757f9ca2
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_prime" name="HyPhy-PRIME" version="@TOOL_VERSION@+galaxy1" profile="19.09">
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3 <description>Property Informed Models of Evolution</description>
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @SYMLINK_FILES@
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11 @HYPHYMPI@ prime
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12 --alignment ./$input_file
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13 @INPUT_TREE@
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14 --code '$gencodeid'
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15 @branch_options@
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16 --pvalue '$p_value'
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17 --properties '$prop_set'
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18 --impute-states '$impute_states'
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19 --output '$prime_output'
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20 @ERRORS@
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21 ]]></command>
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22 <inputs>
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23 <expand macro="inputs"/>
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24 <expand macro="gencode"/>
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25 <expand macro="branches"/>
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26 <param name="prop_set" type="select" label="Biochemical properties to use">
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27 <option value="Atchley">Atchley</option>
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28 <option value="LCAP">LCAP</option>
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29 </param>
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30 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
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31 <param argument="--impute-states" type="boolean" truevalue="Yes" falsevalue="No" label="Use site-level model fits to impute likely character states for each sequence"/>
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32 </inputs>
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33 <outputs>
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34 <data name="prime_output" format="hyphy_results.json" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input_file" ftype="fasta" value="prime-in1.fa"/>
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39 <param name="input_nhx" ftype="nhx" value="prime-in1.nhx"/>
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40 <conditional name="branch_cond">
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41 <param name="branch_sel" value="All"/>
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42 </conditional>
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43 <param name="p_value" value="0.1"/>
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44 <param name="prop_set" value="Atchley"/>
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45 <output name="prime_output" file="prime-out1.json" compare="sim_size"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 PRIME: Property Informed Model of Evolution
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50 ===========================================
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51
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52 What question does this method answer?
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53 --------------------------------------
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54
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55 Does evolution at specific sites in a coding alignment preserve or alter some biochemical properties?
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57 Recommended Applications
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58 ------------------------
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60 Identify biochemical evolutionary constraints or changes with site level resolution: e.g. site 23 is
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61 evolving to conserve residue polarity, but alter it's volume.
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63
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64 Brief description
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65 -----------------
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66
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67 Most methods of coding sequence analysis do not take direct account of the fact that
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68 the rate at which amino-acids are exchanged is different depending on the amino-acids.
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69 While this seems obvious (e.g. radical changes should happen slower), there are many technical reasons
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70 for why the standard assumption of "one-rate for all residues" holds.
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71
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72
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73 Given a set of N amino-acid properties, fit a site-level model where non-synonymous rates
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74 depend on how much a non-synonymous substitution changes the properties
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75 of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )-
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76 lambda_2 * diff_2 (X,Y) -...). When lambda_k > 0, changes in property k
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77 are disfavored and when lambda_k < 0 -- they are promoted. At each site,
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78 N+1 tests are performed (one for each property, and an omnibus test).
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79
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80 Input
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81 -----
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82
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83 1. A *FASTA* sequence alignment.
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84 2. A phylogenetic tree in the *Newick* format
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85
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86 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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87
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88
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89 Output
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90 ------
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91
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92 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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93
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94 A custom visualization module for viewing these results will soon be available at http://vision.hyphy.org/
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95
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96 Further reading
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97 ---------------
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98
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99 http://hyphy.org/methods/selection-methods/#PRIME
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100
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101
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102 Tool options
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103 ------------
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104 ::
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105
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106
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107 --code Which genetic code to use
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108
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109 --branches Which branches should be tested for selection?
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110 All [default] : test all branches
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111
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112 Internal : test only internal branches (suitable for
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113 intra-host pathogen evolution for example, where terminal branches
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114 may contain polymorphism data)
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115
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116 Leaves: test only terminal (leaf) branches
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117
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118 Unlabeled: if the Newick string is labeled using the {} notation,
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119 test only branches without explicit labels
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120 (see http://hyphy.org/tutorials/phylotree/)
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121
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122 --pvalue The significance level used to determine significance
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123
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124 --properties Which property set to use
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125 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]
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126 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]
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127
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128
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129 ]]></help>
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130 <expand macro="citations" />
0
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131 </tool>