Mercurial > repos > iuc > hyphy_bgm

annotate hyphy_bgm.xml @ 32:12c2453e5040 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 11:28:17 +0000
parents a8ea0db2c606
children 5b6b8b08f1a9
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@TOOL_VERSION@+galaxy2" profile="19.09">
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3 <description>- Detecting coevolving sites via Bayesian graphical models</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 ln -s '$bgm_output' ${input_file}.BGM.json &&
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12 hyphy bgm
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13 --alignment $input_file
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14 @INPUT_TREE@
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15 --run_type $datatype.value
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16 #if $datatype.value == "codon":
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17 --code '$datatype.gencodeid'
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18 #end if
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19 #if $datatype.value == "protein":
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20 --baseline_model '$datatype.model'
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21 #end if
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22 @branch_options@
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23 --chain '$chain_length'
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24 --burn_in '$burn_in'
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25 --samples '$samples'
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26 --parents '$parents'
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27 --min_subs '$min_subs'
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28 @ERRORS@
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29 ]]></command>
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30 <inputs>
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31 <expand macro="inputs" />
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32 <conditional name="datatype">
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33 <param name="value" type="select" label="Type of data">
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34 <option value="nucleotide">Nucleotide</option>
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35 <option value="amino-acid">Amino acid</option>
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36 <option value="codon">Codon</option>
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37 </param>
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38 <when value="nucleotide"/>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 <when value="amino-acid">
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40 <expand macro="substitution" />
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41 </when>
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42 <when value="codon">
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43 <expand macro="gencode" />
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44 </when>
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45 </conditional>
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46 <expand macro="branches"/>
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47 <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
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48 <param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
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49 <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
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50 <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" />
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51 <param argument="--min-subs" name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" />
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52 </inputs>
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53 <outputs>
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54 <data name="bgm_output" format="hyphy_results.json" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
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59 <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
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60 <output name="bgm_output" file="bgm-out1.json" compare="sim_size"/>
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61 </test>
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62 </tests>
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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63 <help><![CDATA[
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64
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65 BGM : Bayesian Graphical Models
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66 ===============================
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67
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68 What does this do?
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69 ------------------
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70
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71 This tools identifies groups of sites in the alignments that experience substitutions along the same branches,
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72 i.g. *co-evolve*.
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73
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74 Brief description
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75 -----------------
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76
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77 GM (Bayesian Graphical Model) uses a maximum likelihood ancestral state
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78 reconstruction to map substitution (non-synonymous only for coding data)
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79 events to branches in the phylogeny and then analyzes the joint
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80 distribution of the substitution map using a Bayesian graphical model
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81 (network). Next, a Markov chain Monte Carlo analysis is used to generate
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82 a random sample of network structures from the posterior distribution
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83 given the data. Each node in the network represents a site in the
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84 alignment, and links (edges) between nodes indicate high posterior
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85 support for correlated substitutions at the two sites over time, which
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86 implies coevolution.
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87
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88
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89 Input
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90 -----
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91
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92 1. A *FASTA* sequence alignment.
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93 2. A phylogenetic tree in the *Newick* format
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94
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95 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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96
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97 Output
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98 ------
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99
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100 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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101
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102 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BGM for an example)
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103
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104 Further reading
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105 ---------------
1
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106
5
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107 http://hyphy.org/methods/selection-methods/#BGM
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108
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109
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110 Tool options
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111 ------------
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112 ::
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113
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114 --branches Which branches should be tested for selection?
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115 All [default] : test all branches
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116
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117 Internal : test only internal branches (suitable for
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118 intra-host pathogen evolution for example, where terminal branches
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119 may contain polymorphism data)
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120
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121 Leaves: test only terminal (leaf) branches
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122
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123 Unlabeled: if the Newick string is labeled using the {} notation,
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124 test only branches without explicit labels
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125 (see http://hyphy.org/tutorials/phylotree/)
1
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126
5
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127 --max-parents The maximum number of parents allowed per node, i.e. how many sites
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128 can directly influence substitution patterns at another site
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129 Increasing this number scales complexity nonlinearly
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130 default value: 1
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131
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132 --min-subs The minium number of substitutions per site to include it in the analysis
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133 Filter low complexity (too few substitution) sites
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134 default value: 1
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135
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136 --chains How many MCMC chains to run (does not apply to Variational-Bayes)
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137 default value: 5
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138
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139 --steps MCMC chain length (does not apply to Variational-Bayes)
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140 default value: 100,000
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141
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142 --burn-in MCMC chain burn in (does not apply to Variational-Bayes)
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143 default value: 10,000
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144
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145 --samples MCMC samples to draw (does not apply to Variational-Bayes)
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146 default value: 100
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147
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148
0
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149 ]]></help>
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150 <expand macro="citations">
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151 <citation type="doi">10.1371/journal.pcbi.0030231</citation>
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152 </expand>
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153 </tool>