Mercurial > repos > iuc > hyphy_fade

annotate hyphy_fade.xml @ 25:5e8d0e777033 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:06:34 +0000
parents 17ac281a46d9
children 96817f0fd28b
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1" profile="19.09">
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3 <description>: FUBAR* Approach to Directional Evolution (*Fast
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4 Unconstrained Bayesian Approximation)</description>
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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 hyphy fade
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12 --alignment $input_file
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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13 @INPUT_TREE@
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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14 @branch_options@
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15 --model '$model'
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16 --method '$posteriorEstimationMethod.method'
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17 --grid '$grid_points'
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18 --concentration_parameter '$concentration'
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19 @posteriorEstimationMethod_cmd@
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20 --output '$fade_output'
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21 @ERRORS@
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22 ]]></command>
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23 <inputs>
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24 <expand macro="inputs"/>
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25 <expand macro="branches"/>
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26 <expand macro="substitution"/>
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27 <expand macro="branches"/>
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28 <expand macro="conditional_posteriorEstimationMethod" />
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29 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
16b4a3869bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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30 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
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31 </inputs>
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32 <outputs>
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33 <data name="fade_output" format="hyphy_results.json" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43
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44 FADE : FUBAR Approach to Directional Evolution
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45 ==============================================
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46
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47 What question does this method answer?
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48 --------------------------------------
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49
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50 Which site(s) in an alignment evolve towards to or away from a particular residue.
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51
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52 Recommended Applications
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53 ------------------------
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54
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55 Screen protein sequence alignments where the direction of evolution can be resolved
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56 (via tree rooting, e.g. using an outgroup) to find sites which evolve differently from
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57 a standard protein model (selected by the user), or a gene-average model (GTR) to find
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58 evidence of directional selection.
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59
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60 Brief description
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61 -----------------
1
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62
5
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63 FFADE (FUBAR Approach to Directional Evolution) is a fast method to test
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64 whether or not a subset of sites in a protein alignment evolve towards a
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65 particular residue along a subset of branches at accelerated rates
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66 compared to reference model. FADE uses a random effects model and latent
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67 Dirichlet allocation (LDA) - inspired approximation methods to allocate
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68 sites to rate classes.
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69
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70 Input
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71 -----
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72
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73 1. A *FASTA* sequence alignment of protein sequences.
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74 2. A *rooted* phylogenetic tree in the *Newick* format
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75
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76 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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77
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78
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79 Output
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80 ------
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81
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82 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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83
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84 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FADE for an example)
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85
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86 Further reading
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87 ---------------
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88
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89 http://hyphy.org/methods/selection-methods/#FADE
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90
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91
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92 Tool options
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93 ------------
1
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94
5
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95 ::
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96
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97
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98 --model The baseline substitution model to use
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99 [default] use GTR
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100
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101 --branches Which branches should be tested for selection?
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102 All [default] : test all branches
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103
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104 Internal : test only internal branches (suitable for
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105 intra-host pathogen evolution for example, where terminal branches
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106 may contain polymorphism data)
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107
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108 Leaves: test only terminal (leaf) branches
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109
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110 Unlabeled: if the Newick string is labeled using the {} notation,
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111 test only branches without explicit labels
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112 (see http://hyphy.org/tutorials/phylotree/)
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113
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114 --grid The number of grid points
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115 Smaller : faster
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116 Larger : more precise posterior estimation but slower
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117 default value: 20
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118
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119 --method Inference method to use
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120 Variational-Bayes : 0-th order Variational Bayes approximation; fastest [default]
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121 Metropolis-Hastings : Full Metropolis-Hastings MCMC algorithm; orignal method [slowest]
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122 Collapsed-Gibbs : Collapsed Gibbs sampler [intermediate speed]
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123
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124
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125 --chains How many MCMC chains to run (does not apply to Variational-Bayes)
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126 default value: 5
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127
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128 --chain-length MCMC chain length (does not apply to Variational-Bayes)
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129 default value: 2,000,000
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130
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131 --burn-in MCMC chain burn in (does not apply to Variational-Bayes)
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132 default value: 1,000,000
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133
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134 --samples MCMC samples to draw (does not apply to Variational-Bayes)
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135 default value: 1,000
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136
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137 --concentration_parameter
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138 The concentration parameter of the Dirichlet prior
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139 default value: 0.5
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140
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141
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142
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143 ]]>
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144 </help>
0
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145 <expand macro="citations">
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146 </expand>
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147 </tool>