Mercurial > repos > iuc > hyphy_fade

annotate hyphy_fade.xml @ 32:bfb7df43715d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Tue, 29 Mar 2022 23:54:28 +0000
parents ab9eac75e640
children 2246695d4539
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@TOOL_VERSION@+galaxy1" profile="19.09">
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3 <description>: FUBAR* Approach to Directional Evolution (*Fast
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 Unconstrained Bayesian Approximation)</description>
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5 <macros>
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6 <import>macros.xml</import>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 </macros>
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8 <expand macro="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @SYMLINK_FILES@
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12 hyphy fade
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13 --alignment $input_file
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14 @INPUT_TREE@
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15 @branch_options@
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16 --model '$model'
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17 --method '$posteriorEstimationMethod.method'
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18 --grid '$grid_points'
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19 --concentration_parameter '$concentration'
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20 @posteriorEstimationMethod_cmd@
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21 --output '$fade_output'
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22 @ERRORS@
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23 ]]></command>
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24 <inputs>
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25 <expand macro="inputs"/>
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26 <expand macro="branches"/>
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27 <expand macro="substitution"/>
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28 <expand macro="branches"/>
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29 <expand macro="conditional_posteriorEstimationMethod" />
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30 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
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31 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
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32 </inputs>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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33 <outputs>
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34 <data name="fade_output" format="hyphy_results.json" />
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35 </outputs>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 <tests>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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37 <test>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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40 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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41 </test>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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42 </tests>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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43 <help><![CDATA[
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44
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45 FADE : FUBAR Approach to Directional Evolution
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46 ==============================================
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47
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48 What question does this method answer?
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49 --------------------------------------
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50
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51 Which site(s) in an alignment evolve towards to or away from a particular residue.
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52
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53 Recommended Applications
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54 ------------------------
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55
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56 Screen protein sequence alignments where the direction of evolution can be resolved
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57 (via tree rooting, e.g. using an outgroup) to find sites which evolve differently from
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58 a standard protein model (selected by the user), or a gene-average model (GTR) to find
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59 evidence of directional selection.
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60
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61 Brief description
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62 -----------------
1
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63
5
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64 FFADE (FUBAR Approach to Directional Evolution) is a fast method to test
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65 whether or not a subset of sites in a protein alignment evolve towards a
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66 particular residue along a subset of branches at accelerated rates
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67 compared to reference model. FADE uses a random effects model and latent
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68 Dirichlet allocation (LDA) - inspired approximation methods to allocate
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69 sites to rate classes.
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71 Input
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72 -----
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74 1. A *FASTA* sequence alignment of protein sequences.
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75 2. A *rooted* phylogenetic tree in the *Newick* format
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77 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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80 Output
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81 ------
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82
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83 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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84
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85 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FADE for an example)
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86
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87 Further reading
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88 ---------------
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89
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90 http://hyphy.org/methods/selection-methods/#FADE
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91
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92
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93 Tool options
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94 ------------
1
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95
5
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96 ::
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97
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98
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99 --model The baseline substitution model to use
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100 [default] use GTR
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101
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102 --branches Which branches should be tested for selection?
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103 All [default] : test all branches
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104
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105 Internal : test only internal branches (suitable for
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106 intra-host pathogen evolution for example, where terminal branches
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107 may contain polymorphism data)
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108
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109 Leaves: test only terminal (leaf) branches
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110
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111 Unlabeled: if the Newick string is labeled using the {} notation,
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112 test only branches without explicit labels
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113 (see http://hyphy.org/tutorials/phylotree/)
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114
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115 --grid The number of grid points
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116 Smaller : faster
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117 Larger : more precise posterior estimation but slower
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118 default value: 20
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119
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120 --method Inference method to use
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121 Variational-Bayes : 0-th order Variational Bayes approximation; fastest [default]
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122 Metropolis-Hastings : Full Metropolis-Hastings MCMC algorithm; orignal method [slowest]
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123 Collapsed-Gibbs : Collapsed Gibbs sampler [intermediate speed]
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124
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125
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126 --chains How many MCMC chains to run (does not apply to Variational-Bayes)
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127 default value: 5
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128
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129 --chain-length MCMC chain length (does not apply to Variational-Bayes)
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130 default value: 2,000,000
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131
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132 --burn-in MCMC chain burn in (does not apply to Variational-Bayes)
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133 default value: 1,000,000
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134
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135 --samples MCMC samples to draw (does not apply to Variational-Bayes)
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136 default value: 1,000
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137
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138 --concentration_parameter
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139 The concentration parameter of the Dirichlet prior
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140 default value: 0.5
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141
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142
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143
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144 ]]>
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145 </help>
0
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146 <expand macro="citations">
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147 </expand>
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148 </tool>