Mercurial > repos > iuc > hyphy_relax

annotate hyphy_relax.xml @ 18:b8bdfac5a326 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8f76cb8602f79412152a92b267ee016605ae6b8e"
author iuc
date Wed, 23 Dec 2020 20:04:07 +0000
parents ea64cc9a06e4
children 801547975424
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0" 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="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ln -s '$input_file' relax_input.fa &&
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11 ln -s '$input_nhx' relax_input.nhx &&
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12
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13 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
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14 hyphy relax
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15 --alignment ./relax_input.fa
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16 --tree ./relax_input.nhx
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17 --models '$analysisType'
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18 --code '$gencodeid'
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19 #if $treeAnnotations == "2":
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20 --test TEST
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21 --reference REFERENCE
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22 #else:
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23 --test TEST
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24 #end if
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25 > '$relax_log'
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26 ]]></command>
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27 <inputs>
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28 <expand macro="inputs"/>
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29 <expand macro="gencode"/>
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30 <param argument="--model" name="analysisType" type="select" label="Analysis Type" >
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31 <option value="All">All</option>
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32 <option value="Minimal">Minimal</option>
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33 </param>
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34 <param name="treeAnnotations" type="select" label="Tree Annotations" help = "Is there one or two sets of annotated branches in the Newick file?">
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35 <option value="1">TEST only</option>
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36 <option value="2">TEST and REFERENCE</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data name="relax_log" format="txt"/>
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41 <data name="relax_output" format="hyphy_results.json" from_work_dir="relax_input.fa.RELAX.json"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
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46 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>
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47 <output name="relax_output" file="relax-out1.json" compare="sim_size"/>
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48 </test>
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49 </tests>
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50 <help><![CDATA[
5
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51 RELAX: a test for selection differences
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52 =======================================
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53
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54 What question does this method answer?
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55 --------------------------------------
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56
18
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57 Is there evidence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST)
5
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58 relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically.
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59 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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60 or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation.
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61
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62 Recommended Applications
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63 ------------------------
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64
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65 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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66 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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67
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68
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69 Brief description
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70 -----------------
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71
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72 RELAX (a random effects test of selection relaxation) uses a random
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73 effects branch-site model framework to test whether a set of 'Test'
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74 branches evolves under relaxed selection relative to a set of
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75 'Reference' branches (R), as measured by the relaxation parameter (K).
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76
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77 Input
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78 -----
1
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79
5
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80 1. A *FASTA* sequence alignment.
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81 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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82
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83 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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84
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85
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86 Output
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87 ------
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88
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89 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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90
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91 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/RELAX for an example)
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92
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93 Further reading
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94 ---------------
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95
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96 http://hyphy.org/methods/selection-methods/#RELAX
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98
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99 Tool options
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100 ------------
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101 ::
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102
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103
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104 --code Which genetic code to use
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105
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106 --model Which type of test to run
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107 All : fit 4 different models [default]
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108 Minimal: only perform a 2-model test of relaxation/intensification [faster]
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109
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110
0
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111 ]]></help>
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112 <expand macro="citations">
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113 <citation type="doi">10.1093/molbev/msu400</citation>
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114 </expand>
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115 </tool>