Mercurial > repos > iuc > hyphy_absrel

annotate hyphy_absrel.xml @ 9:cce7b18495e4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
author iuc
date Fri, 27 Mar 2020 13:14:17 -0400
parents f73435dc282b
children 4cc4dbca2f02
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
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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="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_file' absrel_input.fa &&
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10 ln -s '$input_nhx' absrel_input.nhx &&
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11 @HYPHYMPI@ absrel
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12 --alignment ./absrel_input.fa
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13 --tree ./absrel_input.nhx
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14 --code '$gencodeid'
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15 --branches '$branches'
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16 --output '$absrel_output'
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17 #if $log:
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18 > '$absrel_log'
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19 #end if
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20 ;
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21 @CATCH_MPIERR@
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22 ]]></command>
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23 <inputs>
1
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24 <expand macro="inputs"/>
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25 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
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26 <expand macro="gencode"/>
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27 <expand macro="branches"/>
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28 </inputs>
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29 <outputs>
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30 <data name="absrel_log" format="txt">
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31 <filter>log</filter>
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32 </data>
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33 <data name="absrel_output" format="hyphy_results.json" />
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34 </outputs>
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35 <tests>
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36 <test>
1
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37 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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39 <param name="log" value="false"/>
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40 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
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41 </test>
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42 </tests>
1
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43 <help><![CDATA[
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44
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45 aBSREL : Adaptive Branch-Site Random Effects Likelihood
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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 Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?
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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 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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57 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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58
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59 Brief description
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60 -----------------
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61
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62 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive
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63 random effects branch-site model framework to test whether each branch
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64 has evolved under positive selection, using a procedure which infers an
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65 optimal number of rate categories per branch.
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66
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67
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68 Input
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69 -----
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70
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71 1. A *FASTA* sequence alignment.
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72 2. A phylogenetic tree in the *Newick* format
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73
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74 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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77 Output
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78 ------
2
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79
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80 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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81
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82 For each tested branch the analysis will infer the appropriate number of selective regimes,
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83 and whether or not there is statistical evidence of positive selection on that branch.
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84
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85 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)
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86
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87 Further reading
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88 ---------------
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89
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90 http://hyphy.org/methods/selection-methods/#absrel
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91
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92
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93 Tool options
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94 ------------
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95 ::
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96
2
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97
9
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98 --code Which genetic code to use
6
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99
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100 --branches Which branches should be tested for selection?
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101 All [default] : test all branches
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102
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103 Internal : test only internal branches (suitable for
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104 intra-host pathogen evolution for example, where terminal branches
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105 may contain polymorphism data)
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106
6
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107 Leaves: test only terminal (leaf) branches
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108
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109 Unlabeled: if the Newick string is labeled using the {} notation,
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110 test only branches without explicit labels
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111 (see http://hyphy.org/tutorials/phylotree/)
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112
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113
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114
1
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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/msv022</citation>
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118 </expand>
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119 </tool>