Mercurial > repos > iuc > hyphy_relax

annotate hyphy_relax.xml @ 33:7207313de5a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author iuc
date Thu, 18 Aug 2022 13:59:18 +0000
parents 49885a825dc1
children 5eb9d7217640
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_relax" name="HyPhy-RELAX" version="@TOOL_VERSION@+galaxy2" profile="19.09">
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3 <description>Detect relaxed selection in a codon-based
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4 phylogenetic framework</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="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @SYMLINK_FILES@
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12 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
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13 hyphy relax
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14 --alignment ./$input_file
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15 @INPUT_TREE@
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16 --models '$models'
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17 --code '$gencodeid'
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18 --test '$test'
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19 #if $reference:
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20 --reference '$reference'
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21 #end if
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22 @advanced_options@
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23 --output '$relax_output'
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24 @ERRORS@
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25 ]]></command>
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26 <inputs>
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27 <expand macro="inputs"/>
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28 <expand macro="gencode"/>
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29 <param argument="--models" type="select" label="Analysis Type" >
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30 <option value="All">All</option>
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31 <option value="Minimal">Minimal</option>
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32 </param>
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33 <param argument="--test" type="text" value="Unlabeled branches" optional="false" label="Branches to use as the test set">
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34 <sanitizer invalid_char="">
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35 <valid initial="default" />
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36 </sanitizer>
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37 </param>
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38 <param argument="--reference" type="text" optional="true" label="Branches to use as the reference set">
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39 <sanitizer invalid_char="">
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40 <valid initial="default" />
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41 </sanitizer>
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42 </param>
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43 <expand macro="srv" />
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44 </inputs>
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45 <outputs>
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46 <data name="relax_output" format="hyphy_results.json"/>
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47 <expand macro="alternative_model_output" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
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52 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>
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53 <param name="test" value="TEST" />
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54 <output name="relax_output" file="relax-out1.json" compare="sim_size"/>
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55 </test>
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56 <test>
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57 <param name="input_file" ftype="nex" value="relax-in2.nex"/>
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58 <param name="test" value="PR" />
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59 <conditional name="advanced">
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60 <param name="srv_options" value="specify" />
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61 <param name="save_alternative_model" value="true" />
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62 <param name="srv" value="false" />
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63 </conditional>
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64 <output name="relax_output" file="relax-out2-1.json" compare="sim_size"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 RELAX: a test for selection differences
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69 =======================================
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70
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71 What question does this method answer?
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72 --------------------------------------
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73
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74 Is there evidence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST)
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75 relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically.
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76 We note that the RELAX framework can perform both this specific hypothesis test as well as fit a suite of descriptive models which address,
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77 or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation.
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78
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79 Recommended Applications
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80 ------------------------
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81
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82 1. Testing for a systematic shift (relaxation / intensification) in the distribution of selection pressure associated with major biological transitions such as hosting switching in viruses, lifestyle evolution in bacteria (i.e. transition from free-living to endosymbiotic lifestyle
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83 2. Comparing selective regimes between two subsets of branches in the tree, e.g. to investigate selective differences due an environmental/phenotypic changes.
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84
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85
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86 Brief description
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87 -----------------
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88
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89 RELAX (a random effects test of selection relaxation) uses a random
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90 effects branch-site model framework to test whether a set of 'Test'
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91 branches evolves under relaxed selection relative to a set of
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92 'Reference' branches (R), as measured by the relaxation parameter (K).
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93
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94 Input
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95 -----
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96
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97 1. A *FASTA* sequence alignment.
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98 2. A phylogenetic tree in the *Newick* format that is further partitioned into one or two groups (_TEST_ or _TEST_ and _REFERENCE_). See http://hyphy.org/tutorials/phylotree/
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99
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100 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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101
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102
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103 Output
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104 ------
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105
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106 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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107
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108 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/RELAX for an example)
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109
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110 Further reading
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111 ---------------
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112
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113 http://hyphy.org/methods/selection-methods/#RELAX
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114
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115
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116 Tool options
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117 ------------
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118 ::
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119
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120
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121 --code Which genetic code to use
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122
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123 --model Which type of test to run
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124 All : fit 4 different models [default]
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125 Minimal: only perform a 2-model test of relaxation/intensification [faster]
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126
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127
0
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128 ]]></help>
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129 <expand macro="citations">
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130 <citation type="doi">10.1093/molbev/msu400</citation>
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131 </expand>
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132 </tool>