Mercurial > repos > iuc > hyphy_gard

annotate hyphy_gard.xml @ 35:69864510d68a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:42:01 +0000
parents 02b1656d82a1
children
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02b1656d82a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_gard" name="HyPhy-GARD" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Genetic Algorithm for Recombination Detection</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @SYMLINK_FILES_NO_TREE@
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10 @HYPHYMPI@ gard
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11 --alignment $input_file
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12 --type '$datatype.value'
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13 #if str($datatype.value) == 'codon':
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14 --code '$datatype.gencodeid'
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15 #elif str($datatype.value) == 'amino-acid':
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16 --model '$datatype.model'
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17 #end if
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18 #if str($rate_cond.rate):
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19 --rv '$rate_cond.rate'
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20 --rate-classes '$rate_cond.rate_classes'
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21 #end if
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22 #if $advanced_options.max_breakpoints:
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23 --max-breakpoints '$advanced_options.max_breakpoints'
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24 #end if
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25 #if $advanced_options.mode:
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26 --mode '$advanced_options.mode'
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27 #end if
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28 ENV="TOLERATE_NUMERICAL_ERRORS=1;"
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29 --output '$gard_output_json'
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30 --output-lf '$gard_output'
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31 > gard_stdout.md
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32 @ERRORS@
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33 ]]></command>
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34 <inputs>
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35 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="Input FASTA or NEXUS file." />
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36 <conditional name="datatype">
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37 <param argument="--type" name="value" type="select" label="Alignment kind" help="Select the type of data to perform screening on.">
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38 <option value="nucleotide">Nucleotide</option>
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39 <option value="amino-acid">Amino acid</option>
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40 <option value="codon">Codon</option>
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41 </param>
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42 <when value="nucleotide"/>
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43 <when value="amino-acid">
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44 <expand macro="substitution" argument="--model" />
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45 </when>
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46 <when value="codon">
0
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47 <expand macro="gencode" />
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48 </when>
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49 </conditional>
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50 <conditional name="rate_cond">
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51 <param argument="--rv" name="rate" type="select" label="Rate variation" help="Specify how site-to-site rate variation should be modeled.">
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52 <option value="">None</option>
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53 <option value="GDD">General Discrete</option>
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54 <option value="Gamma">Beta-Gamma</option>
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55 </param>
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56 <when value=""/>
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57 <when value="GDD">
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58 <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" help="The number of discrete rate classes to use for modeling site-to-site rate variation." />
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59 </when>
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60 <when value="Gamma">
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61 <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" help="The number of discrete rate classes to use for modeling site-to-site rate variation." />
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62 </when>
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63 </conditional>
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64 <section name="advanced_options" title="Advanced Options" expanded="false">
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65 <param argument="--max-breakpoints" type="integer" value="10000" min="1" max="10000" label="Maximum number of breakpoints to consider" help="The maximum number of breakpoints the genetic algorithm will consider during its search."/>
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66 <param argument="--mode" type="select" label="Run mode" help="Select the run mode for GARD. 'Normal' uses default optimization and convergence settings, while 'Faster' reduces precision and relaxes convergence for quicker results.">
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67 <option value="Normal">Normal</option>
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68 <option value="Faster">Faster</option>
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69 </param>
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70 </section>
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71 </inputs>
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72 <outputs>
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73 <data name="gard_output" format="nex" />
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74 <data name="gard_output_json" format="hyphy_results.json" label="${tool.name} on ${on_string}: gard_output_json" />
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75 <data name="gard_md_report" format="markdown" from_work_dir="gard_stdout.md" label="GARD Report (Markdown) for ${tool.name} on ${on_string}" />
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76 </outputs>
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77 <tests>
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78 <test expect_num_outputs="3">
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79 <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
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80 <output name="gard_output" file="gard-out1.nex" compare="sim_size"/>
35
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81 <output name="gard_output_json">
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82 <assert_contents>
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83 <has_text text='"potentialBreakpoints":21'/>
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84 </assert_contents>
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85 </output>
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86 <output name="gard_md_report">
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87 <assert_contents>
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88 <has_text text="Done with 2 breakpoint analysis."/>
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89 </assert_contents>
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90 </output>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 GARD : Genetic Algorithms for Recombination Detection.
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95 ======================================================
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96
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97 **What does this do?**
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98
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99 This tool screens an alignment of sequences for evidence of recombination in one or more sequences.
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100 The main idea is that if sufficient recombination has occurred, then no single phylogenetic tree will
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101 properly fit the entire length of the alignment and instead a separate tree will be preferred for each *nonrecombinant* segment.
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102
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103 **Methodology**
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104
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105 GARD (Genetic Algorithm for Recombination Detection) implements a heuristic approach to screening alignments of sequences for recombination. It uses the CHC genetic algorithm to search for phylogenetic incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc tests run to distinguish topological incongruence from rate-variation.
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106
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107 **The Intuition**
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108
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109 Imagine you have a long DNA sequence, and you suspect that different parts of this sequence might have evolved under different evolutionary histories due to recombination events. If you try to build a single phylogenetic tree for the entire sequence, it might not accurately represent the relationships between the organisms.
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110
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111 GARD addresses this by looking for "breakpoints" in the sequence where the evolutionary history changes. It uses a genetic algorithm to efficiently search for these breakpoints and then infers separate phylogenetic trees for each segment between the breakpoints. This allows for a more accurate understanding of the evolutionary history of recombinant sequences.
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112
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113 **Input**
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114
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115 A *FASTA* sequence alignment
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116
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117 **Output**
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118
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119 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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120
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121 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/GARD for an example)
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122
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123 A Markdown file with a summary of the analysis.
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124
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125 **Further reading**
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126
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127
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128 **Tool options**
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129 ::
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130
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131
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132 --type type of alignment to screen
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133 Nucleotide [default].
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134 Assumes aligned nucleotide data and screens the alignment using
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135 the general time reversible model of sequence evolution.
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136 This is the fastest option
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137 Protein
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138 Assumes aligned aminoacid sequences. One of several protein
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139 substitution models may be used to screen the alignment.
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140 Codon
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141 Assumes an in-frame coding sequence alignment.
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142 The Muse-Gaut 94 (GTR) model will be used to screen the alignment.
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143 Selecting this option will dramatically increase run times.
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144
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145
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146 --code Genetic code/translation table to use (for codon alignments).
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147 Default value: Universal
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148
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149 --model The substitution model to use (for protein alignments).
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150 default value: JTT
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151
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152 --rv Site to site rate variation.
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153 None: Constant rates.
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154 Gamma: Unit mean gamma distribution discretized into N rates.
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155 GDD: General discrete distribution on N rates.
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156
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157 --rate-classes How many site rate classes to use (if GDD or Beta-Gamma are selected)
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158 default value: 4
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159
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160 --max-breakpoints Maximum number of breakpoints to consider.
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161
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162 --mode Run mode.
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163 Normal: Default optimization and convergence settings.
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164 Faster: Reduce individual optimization precision and relax convergence settings.
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165
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166 ]]>
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167 </help>
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168 <expand macro="citations">
01690807ace8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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169 <citation type="doi">10.1093/molbev/msl051</citation>
01690807ace8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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170 </expand>
01690807ace8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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171 </tool>