Mercurial > repos > iuc > hyphy_fade

annotate hyphy_fade.xml @ 15:00a82d4c1f82 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
author iuc
date Fri, 18 Sep 2020 20:58:17 +0000
parents 6550fe0cb394
children 8f4c950e43a9
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1 <?xml version="1.0"?>
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ea7ab5a8b530 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6b2cd926797bb94fba9d0e319a2dbcff6ee37735"
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2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
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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>
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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[
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 ln -s '$input_file' fade_input.fa &&
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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11 ln -s '$input_nhx' fade_input.nhx &&
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12 hyphy fade
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13 --alignment ./fade_input.fa
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 --tree ./fade_input.nhx
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15 --branches '$branches'
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16 --model '$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 > '$fade_log'
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23 ]]></command>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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24 <inputs>
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25 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
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26 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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27 <expand macro="branches"/>
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28 <expand macro="substitution"/>
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29 <expand macro="branches"/>
5
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30 <expand macro="conditional_posteriorEstimationMethod" />
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31 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
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32 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
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33 </inputs>
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34 <outputs>
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35 <data name="fade_log" format="txt"/>
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36 <data name="fade_output" format="hyphy_results.json" />
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37 </outputs>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <tests>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 <test>
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40 <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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41 <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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42 <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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43 </test>
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44 </tests>
c6774455f9c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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45 <help><![CDATA[
5
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46
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47 FADE : FUBAR Approach to Directional Evolution
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48 ==============================================
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49
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50 What question does this method answer?
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51 --------------------------------------
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52
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53 Which site(s) in an alignment evolve towards to or away from a particular residue.
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54
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55 Recommended Applications
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56 ------------------------
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57
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58 Screen protein sequence alignments where the direction of evolution can be resolved
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59 (via tree rooting, e.g. using an outgroup) to find sites which evolve differently from
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60 a standard protein model (selected by the user), or a gene-average model (GTR) to find
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61 evidence of directional selection.
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62
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63 Brief description
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64 -----------------
1
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65
5
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66 FFADE (FUBAR Approach to Directional Evolution) is a fast method to test
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67 whether or not a subset of sites in a protein alignment evolve towards a
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68 particular residue along a subset of branches at accelerated rates
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69 compared to reference model. FADE uses a random effects model and latent
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70 Dirichlet allocation (LDA) - inspired approximation methods to allocate
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71 sites to rate classes.
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72
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73 Input
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74 -----
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75
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76 1. A *FASTA* sequence alignment of protein sequences.
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77 2. A *rooted* phylogenetic tree in the *Newick* format
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78
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79 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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80
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81
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82 Output
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83 ------
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84
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85 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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86
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87 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FADE for an example)
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88
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89 Further reading
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90 ---------------
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91
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92 http://hyphy.org/methods/selection-methods/#FADE
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93
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94
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95 Tool options
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96 ------------
1
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97
5
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98 ::
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99
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100
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101 --model The baseline substitution model to use
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102 [default] use GTR
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103
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104 --branches Which branches should be tested for selection?
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105 All [default] : test all branches
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106
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107 Internal : test only internal branches (suitable for
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108 intra-host pathogen evolution for example, where terminal branches
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109 may contain polymorphism data)
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110
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111 Leaves: test only terminal (leaf) branches
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112
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113 Unlabeled: if the Newick string is labeled using the {} notation,
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114 test only branches without explicit labels
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115 (see http://hyphy.org/tutorials/phylotree/)
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116
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117 --grid The number of grid points
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118 Smaller : faster
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119 Larger : more precise posterior estimation but slower
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120 default value: 20
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121
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122 --method Inference method to use
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123 Variational-Bayes : 0-th order Variational Bayes approximation; fastest [default]
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124 Metropolis-Hastings : Full Metropolis-Hastings MCMC algorithm; orignal method [slowest]
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125 Collapsed-Gibbs : Collapsed Gibbs sampler [intermediate speed]
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126
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127
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128 --chains How many MCMC chains to run (does not apply to Variational-Bayes)
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129 default value: 5
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130
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131 --chain-length MCMC chain length (does not apply to Variational-Bayes)
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132 default value: 2,000,000
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133
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134 --burn-in MCMC chain burn in (does not apply to Variational-Bayes)
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135 default value: 1,000,000
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136
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137 --samples MCMC samples to draw (does not apply to Variational-Bayes)
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138 default value: 1,000
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139
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140 --concentration_parameter
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141 The concentration parameter of the Dirichlet prior
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142 default value: 0.5
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143
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144
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145
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146 ]]>
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147 </help>
0
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148 <expand macro="citations">
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149 </expand>
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150 </tool>