Mercurial > repos > iuc > hyphy_slac

annotate hyphy_slac.xml @ 35:2753a5c7597a 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 15:16:14 +0000
parents 365e33adf3a4
children
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35
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1 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Single Likelihood Ancestor Counting</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@
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10 hyphy slac
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11 --alignment ./$input_file
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12 @INPUT_TREE@
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13 --code '$gencodeid'
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14 @branch_options@
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15 --samples '$number_of_samples'
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16 --pvalue '$p_value'
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17 --output '$slac_output'
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18 @ERRORS@
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19 ]]></command>
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20 <inputs>
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21 <expand macro="inputs"/>
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22 <expand macro="gencode"/>
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23 <expand macro="branches"/>
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24 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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25 <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
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26 </inputs>
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27 <outputs>
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28 <data name="slac_output" format="hyphy_results.json" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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33 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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34 <output name="slac_output">
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35 <assert_contents>
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36 <has_size value="280000" delta="8000"/>
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37 <has_text text="tested"/>
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38 <has_text text="sample-median"/>
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39 <has_text text="sample-97.5"/>
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40 </assert_contents>
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41 </output>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 SLAC : Single Likelihood Ancestor Counting
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46 ==========================================
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47
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48 What question does this method answer?
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49 --------------------------------------
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51 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
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52
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53 Recommended Applications
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54 ------------------------
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55
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56 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
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57 (or balancing selection), including adaptive immune escape by viruses. As such, SLAC is ideally suited to identify sites under positive selection which
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58 represent candidate sites subject to strong selective pressures across the entire phylogeny.
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59 SLAC provides legacy functionality as a counting-based method adapted for phylogenetic applications.
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60 In general, this method will be the least statistically robust (compared to FEL or FUBAR), but it is the most directly interpretable.
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61
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62 Brief description
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63 -----------------
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64
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65 SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood
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66 ancestral state reconstruction and minimum path substitution counting to
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67 estimate site - level dS and dN, and applies a simple binomial - based
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68 test to test if dS differs drom dN. The estimates aggregate information
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69 over all branches, so the signal is derived from pervasive
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70 diversification or conservation. A subset of branches can be selected
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71 for testing as well.
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72
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73 Input
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74 -----
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75
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76 1. A *FASTA* sequence alignment.
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77 2. A phylogenetic tree in the *Newick* format
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78
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79 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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80
2
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81
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82 Output
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83 ------
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84
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85 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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86
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87 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/SLAC for an example)
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88
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89 Further reading
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90 ---------------
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91
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92 http://hyphy.org/methods/selection-methods/#SLAC
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93
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94
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95 Tool options
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96 ------------
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97 ::
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98
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99
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100 --code Which genetic code to use
2
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101
6
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102 --branches Which branches should be tested for selection?
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103 All [default] : test all branches
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104
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105 Internal : test only internal branches (suitable for
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106 intra-host pathogen evolution for example, where terminal branches
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107 may contain polymorphism data)
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108
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109 Leaves: test only terminal (leaf) branches
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110
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111 Unlabeled: if the Newick string is labeled using the {} notation,
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112 test only branches without explicit labels
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113 (see http://hyphy.org/tutorials/phylotree/)
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114
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115 --pvalue The significance level used to determine significance
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116
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117 --samples Draw this many alternative ancestral state reconstructions
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118 to evaluate uncertainty
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119
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120 ]]>
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121 </help>
0
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122 <expand macro="citations">
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123 <citation type="doi">10.1093/molbev/msi105</citation>
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124 </expand>
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125 </tool>