Mercurial > repos > iuc > hyphy_slac

annotate hyphy_slac.xml @ 34:1467fb7e162d 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 13:56:28 +0000
parents 365e33adf3a4
children 2753a5c7597a
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@TOOL_VERSION@+galaxy1" profile="19.09">
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3 <description>Single Likelihood Ancestor Counting</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @SYMLINK_FILES@
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11 hyphy slac
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12 --alignment ./$input_file
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13 @INPUT_TREE@
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14 --code '$gencodeid'
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15 @branch_options@
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16 --samples '$number_of_samples'
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17 --pvalue '$p_value'
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18 --output '$slac_output'
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19 @ERRORS@
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20 ]]></command>
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21 <inputs>
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22 <expand macro="inputs"/>
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23 <expand macro="gencode"/>
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24 <expand macro="branches"/>
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25 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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26 <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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27 </inputs>
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28 <outputs>
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29 <data name="slac_output" format="hyphy_results.json" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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34 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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35 <output name="slac_output" file="slac-out1.json" compare="sim_size"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 SLAC : Single Likelihood Ancestor Counting
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40 ==========================================
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42 What question does this method answer?
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43 --------------------------------------
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45 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
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47 Recommended Applications
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48 ------------------------
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50 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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51 (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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52 represent candidate sites subject to strong selective pressures across the entire phylogeny.
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53 SLAC provides legacy functionality as a counting-based method adapted for phylogenetic applications.
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54 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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56 Brief description
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57 -----------------
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59 SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood
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60 ancestral state reconstruction and minimum path substitution counting to
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61 estimate site - level dS and dN, and applies a simple binomial - based
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62 test to test if dS differs drom dN. The estimates aggregate information
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63 over all branches, so the signal is derived from pervasive
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64 diversification or conservation. A subset of branches can be selected
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65 for testing as well.
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67 Input
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68 -----
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70 1. A *FASTA* sequence alignment.
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71 2. A phylogenetic tree in the *Newick* format
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73 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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75
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76 Output
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77 ------
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79 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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81 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/SLAC for an example)
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83 Further reading
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84 ---------------
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86 http://hyphy.org/methods/selection-methods/#SLAC
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87
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88
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89 Tool options
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90 ------------
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91 ::
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92
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93
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94 --code Which genetic code to use
2
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95
6
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96 --branches Which branches should be tested for selection?
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97 All [default] : test all branches
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98
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99 Internal : test only internal branches (suitable for
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100 intra-host pathogen evolution for example, where terminal branches
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101 may contain polymorphism data)
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102
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103 Leaves: test only terminal (leaf) branches
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104
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105 Unlabeled: if the Newick string is labeled using the {} notation,
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106 test only branches without explicit labels
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107 (see http://hyphy.org/tutorials/phylotree/)
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108
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109 --pvalue The significance level used to determine significance
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110
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111 --samples Draw this many alternative ancestral state reconstructions
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112 to evaluate uncertainty
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113
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114 ]]>
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115 </help>
0
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116 <expand macro="citations">
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117 <citation type="doi">10.1093/molbev/msi105</citation>
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118 </expand>
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119 </tool>