annotate hyphy_absrel.xml @ 34:a6619171428e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author iuc
date Thu, 18 Aug 2022 14:05:48 +0000
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
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3 <description>adaptive Branch Site Random Effects Likelihood</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 ln -s '$absrel_output' ${input_file}.aBSREL.json &&
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12 @HYPHYMPI@ absrel
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13 --alignment ./$input_file
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14 @INPUT_TREE@
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15 --code '$gencodeid'
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16 @branch_options@
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17 --output '$absrel_output'
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18 --multiple-hits $multiple_hits
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19 $srv
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20 @ERRORS@
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21 ]]></command>
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22 <inputs>
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23 <expand macro="inputs"/>
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24 <expand macro="gencode"/>
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25 <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
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26 <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
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27 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
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28 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
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29 </param>
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30 <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" />
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31 <expand macro="branches"/>
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32 </inputs>
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33 <outputs>
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34 <data name="absrel_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 <param name="multiple_hits" value="None" />
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41 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
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42 </test>
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43 <test>
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44 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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45 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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46 <param name="multiple_hits" value="Double" />
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47 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
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48 </test>
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49 <test>
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50 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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52 <param name="multiple_hits" value="Double" />
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53 <param name="srv" value="--srv Yes" />
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54 <output name="absrel_output" file="absrel-out2.json" compare="sim_size"/>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58
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59 aBSREL : Adaptive Branch-Site Random Effects Likelihood
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60 =======================================================
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61
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62 What question does this method answer?
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63 --------------------------------------
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64
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65 Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?
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66
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67 Recommended Applications
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68 ------------------------
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69
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70 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
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71 2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences)
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72
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73 Brief description
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74 -----------------
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75
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76 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive
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77 random effects branch-site model framework to test whether each branch
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78 has evolved under positive selection, using a procedure which infers an
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79 optimal number of rate categories per branch.
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80
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81
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82 Input
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83 -----
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84
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85 1. A *FASTA* sequence alignment.
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86 2. A phylogenetic tree in the *Newick* format
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87
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88 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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89
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90
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91 Output
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92 ------
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93
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94 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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95
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96 For each tested branch the analysis will infer the appropriate number of selective regimes,
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97 and whether or not there is statistical evidence of positive selection on that branch.
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98
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99 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)
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100
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101 Further reading
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102 ---------------
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103
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104 http://hyphy.org/methods/selection-methods/#absrel
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105
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106
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107 Tool options
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108 ------------
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109 ::
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110
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111
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112 --code Which genetic code to use
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113
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114 --branches Which branches should be tested for selection?
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115 All [default] : test all branches
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116
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117 Internal : test only internal branches (suitable for
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118 intra-host pathogen evolution for example, where terminal branches
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119 may contain polymorphism data)
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120
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121 Leaves: test only terminal (leaf) branches
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122
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123 Unlabeled: if the Newick string is labeled using the {} notation,
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124 test only branches without explicit labels
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125 (see http://hyphy.org/tutorials/phylotree/)
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126
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127
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128
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129 ]]></help>
0
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130 <expand macro="citations">
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131 <citation type="doi">10.1093/molbev/msv022</citation>
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132 </expand>
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133 </tool>