Mercurial > repos > iuc > hyphy_slac

annotate hyphy_slac.xml @ 24:ec499ddce7a9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:28:55 +0000
parents dc9e52b2d0e1
children 0c6724c345d9
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0" 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 <token name="@OPERATION@">SLAC</token>
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7 <token name="@operation@">slac</token>
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8 </macros>
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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 hyphy slac
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13 --alignment ./$input_file
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14 #if $input_nhx:
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15 --tree ./input.nhx
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16 #end if
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17 --code '$gencodeid'
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18 --branches '$branches'
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19 --samples '$number_of_samples'
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20 --pvalue '$p_value'
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21 --output '$slac_output'
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22 > '$slac_log' ;
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23 @CATCH_ERROR@
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24 ]]></command>
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25 <inputs>
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26 <expand macro="inputs"/>
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27 <expand macro="gencode"/>
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28 <expand macro="branches"/>
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29 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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30 <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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31 </inputs>
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32 <outputs>
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33 <data name="slac_log" format="txt"/>
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34 <data name="slac_output" format="hyphy_results.json" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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39 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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40 <output name="slac_output" file="slac-out1.json" compare="sim_size"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 SLAC : Single Likelihood Ancestor Counting
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45 ==========================================
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47 What question does this method answer?
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48 --------------------------------------
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50 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?
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52 Recommended Applications
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53 ------------------------
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54
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55 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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56 (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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57 represent candidate sites subject to strong selective pressures across the entire phylogeny.
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58 SLAC provides legacy functionality as a counting-based method adapted for phylogenetic applications.
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59 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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60
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61 Brief description
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62 -----------------
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63
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64 SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood
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65 ancestral state reconstruction and minimum path substitution counting to
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66 estimate site - level dS and dN, and applies a simple binomial - based
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67 test to test if dS differs drom dN. The estimates aggregate information
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68 over all branches, so the signal is derived from pervasive
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69 diversification or conservation. A subset of branches can be selected
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70 for testing as well.
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71
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72 Input
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73 -----
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74
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75 1. A *FASTA* sequence alignment.
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76 2. A phylogenetic tree in the *Newick* format
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77
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78 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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79
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80
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81 Output
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82 ------
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83
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84 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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85
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86 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/SLAC for an example)
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87
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88 Further reading
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89 ---------------
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90
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91 http://hyphy.org/methods/selection-methods/#SLAC
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92
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93
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94 Tool options
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95 ------------
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96 ::
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97
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98
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99 --code Which genetic code to use
2
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100
6
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101 --branches Which branches should be tested for selection?
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102 All [default] : test all branches
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103
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104 Internal : test only internal branches (suitable for
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105 intra-host pathogen evolution for example, where terminal branches
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106 may contain polymorphism data)
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107
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108 Leaves: test only terminal (leaf) branches
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109
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110 Unlabeled: if the Newick string is labeled using the {} notation,
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111 test only branches without explicit labels
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112 (see http://hyphy.org/tutorials/phylotree/)
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113
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114 --pvalue The significance level used to determine significance
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115
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116 --samples Draw this many alternative ancestral state reconstructions
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117 to evaluate uncertainty
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118
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119 ]]>
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120 </help>
0
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121 <expand macro="citations">
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122 <citation type="doi">10.1093/molbev/msi105</citation>
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123 </expand>
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124 </tool>