Mercurial > repos > iuc > hyphy_gard

annotate hyphy_gard.xml @ 34:5b777002c2de draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:16:52 +0000
parents 26834f8534f9
children
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5b777002c2de 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 ln -s '$input_file' input.$input_file.extension &&
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10 #set $input_file = 'input.%s' % $input_file.extension
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11 @HYPHYMPI@ gard
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12 --alignment ./$input_file
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13 --type '$datatype.value'
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14 #if str($datatype.value) == 'codon':
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15 --code '$datatype.gencodeid'
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16 #elif str($datatype.value) == 'amino-acid':
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17 --model '$datatype.model'
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18 #end if
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19 #if str($rate_cond.rate):
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20 --rv '$rate_cond.rate'
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21 --rate-classes '$rate_cond.rate_classes'
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22 #end if
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23 --output '$translated'
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24 --output-lf '$gard_output'
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25 @ERRORS@
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26 ]]></command>
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27 <inputs>
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28 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" />
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29 <conditional name="datatype">
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30 <param argument="--type" name="value" type="select" label="Alignment kind">
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31 <option value="nucleotide">Nucleotide</option>
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32 <option value="amino-acid">Amino acid</option>
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33 <option value="codon">Codon</option>
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34 </param>
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35 <when value="nucleotide"/>
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36 <when value="amino-acid">
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37 <expand macro="substitution" argument="--model" />
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38 </when>
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39 <when value="codon">
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40 <expand macro="gencode" />
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41 </when>
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42 </conditional>
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43 <conditional name="rate_cond">
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44 <param argument="--rv" name="rate" type="select" label="Rate variation">
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45 <option value="">None</option>
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46 <option value="GDD">General Discrete</option>
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47 <option value="Gamma">Beta-Gamma</option>
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48 </param>
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49 <when value=""/>
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50 <when value="GDD">
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51 <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
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52 </when>
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53 <when value="Gamma">
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54 <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
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55 </when>
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56 </conditional>
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57 </inputs>
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58 <outputs>
1
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59 <data name="gard_output" format="nex" />
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60 <data name="translated" format="hyphy_results.json" label="${tool.name} on ${on_string}: Translated" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
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65 <output name="gard_output" file="gard-out1.nex" compare="sim_size"/>
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66 <output name="translated" file="gard-out1.json" compare="sim_size"/>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70
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71 GARD : Genetic Algorithms for Recombination Detection.
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72 ======================================================
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73
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74 What does this do?
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75 ------------------
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76
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77 This tools screens an alignment of sequences for evidence of recombination in one or more sequences.
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78 The main idea is that if sufficient recombination has occurred, then no single phylogenetic tree will
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79 properly fit the entire length of the alignment and instead a separate tree will be preferred for each *nonrecombinant* segment.
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80
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81 Brief description
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82 -----------------
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83
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84 This analysis implements a heuristic approach to screening alignments of sequences for
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85 recombination, by using the CHC genetic algorithm (GA) to search for
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86 phylogenetic incongruence among different partitions of the data. The
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87 number of partitions is determined using a step-up procedure, while the
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88 placement of breakpoints is searched for with the GA. The best fitting
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89 model (based on c-AIC) is returned; and additional post-hoc tests run to
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90 distinguish topological incongruence from rate-variation.
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91
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92 For each identified breakpoint, the support for its placement is calculated, and for each
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93 non-recombinant fragment, a phylogenetic tree is inferred (using neighbor joining) and returned.
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94
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95 Input
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96 -----
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97
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98 A *FASTA* sequence alignment
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99
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100 Output
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101 ------
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102
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103 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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104
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105 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/GARD for an example)
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106
1
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107
5
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108 Tool options
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109 ------------
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110 ::
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111
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112
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113 --type type of alignment to screen
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114 Nucleotide [default].
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115 Assumes aligned nucleotide data and screens the alignment using
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116 the general time reversible model of sequence evolution.
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117 This is the fastest option
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118 Protein
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119 Assumes aligned aminoacid sequences. One of several protein
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120 substitution models may be used to screen the alignment.
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121 Codon
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122 Assumes an in-frame coding sequence alignment.
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123 The Muse-Gaut 94 (GTR) model will be used to screen the alignment.
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124 Selecting this option will dramatically increase run times.
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125
1
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126
5
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127 --code Genetic code/translation table to use (for codon alignments).
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128 Default value: Universal
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129
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130 --model The substitution model to use (for protein alignments).
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131 default value: JTT
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132
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133 --rv The discrete distribution to use for modeling site to site rate variation.
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134
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135 None [default]
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136 No rate variation. This is the fastest option in terms of run time, but
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137 using it can result in false positives if there is significant site-to-site
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138 rate variation
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139 GDD
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140 Use the general discrete distribution on N bins
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141 Beta-Gamma
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142 Use a discretized gamma with weights partitioned by a discretized beta
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143 (see doi.org/10.1093/molbev/msi009)
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144
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145 --rate-classes How many site rate classes to use (if GDD or Beta-Gamma are selected)
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146 default value: 4
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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">10.1093/molbev/msl051</citation>
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152 </expand>
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153 </tool>