Mercurial > repos > iuc > hyphy_sm19

annotate hyphy_sm19.xml @ 31:1527f00ddf7f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
author iuc
date Sat, 27 Nov 2021 11:32:54 +0000
parents 23b041c0d7d2
children 00b4cf477625
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="@TOOL_VERSION@+galaxy1" profile="19.09">
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3 <description>Partition Tree using Modified Slatkin-Maddison Test</description>
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ln -s '$input_file' sm19_input.nhx &&
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11 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf ./sm19_input.nhx
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12 #for $n, $partition in enumerate($partitions):
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13 '${partition.label}'
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14 '${partition.regex}'
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15 #end for
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16 $replicates
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17 --output '$sm19_output'
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18 @ERRORS@
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19 ]]></command>
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20 <inputs>
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21 <param name="input_file" type="data" format="nhx,newick,nexus" label="Input tree"/>
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22 <repeat name="partitions" min="2" max="50" title="Partitions">
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23 <param name="label" type="text" label="Partition label"/>
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24 <param name="regex" type="text" label="Regular expression">
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25 <sanitizer>
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26 <valid initial="string.printable">
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27 <remove value="'"/>
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28 </valid>
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29 <mapping initial="none">
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30 <add source="'" target="__sq__"/>
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31 </mapping>
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32 </sanitizer>
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33 </param>
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34 </repeat>
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35 <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
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36 </inputs>
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37 <outputs>
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38 <data name="sm19_output" format="hyphy_results.json" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
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43 <param name="replicates" value="1000"/>
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44 <repeat name="partitions">
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45 <param name="label" value="Blood"/>
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46 <param name="regex" value="B[0-9]+"/>
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47 </repeat>
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48 <repeat name="partitions">
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49 <param name="label" value="Semen"/>
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50 <param name="regex" value="S[0-9]+"/>
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51 </repeat>
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52 <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/>
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53 </test>
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54 <test>
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55 <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/>
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56 <param name="replicates" value="1000"/>
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57 <repeat name="partitions">
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58 <param name="label" value="Blood"/>
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59 <param name="regex" value="B[0-9]+"/>
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60 </repeat>
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61 <repeat name="partitions">
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62 <param name="label" value="Semen"/>
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63 <param name="regex" value="S[0-9]+"/>
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64 </repeat>
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65 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
5
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69
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70 SM2019 : Structured Slatkin-Maddison
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71 ====================================
9
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72
5
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73 What does this do?
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74 ------------------
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75
9
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76 Test for evidence of genetically segregated populations, using a "detuned" version of
5
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77 the Slatkin-Maddison test.
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78
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79 Brief description
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80 -----------------
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81
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82 This analysis implements canonical and modified versions of the
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83 Slatkin-Maddison phylogeny based test for population segregation. The
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84 test estimates the minimum number of migration events using maximum
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85 parsimony, and then evaluating whether or not this number is lower than
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86 expected in a panmictic or unstructured population using permutation
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87 tests
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88
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89 Input
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90 -----
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91
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92 1. A phylogenetic tree in the *Newick* format
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93
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94 Note: assumes that leaf names that can be partitioned into sets using regular expressions
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95
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96 For example
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97
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98 ::
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99
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100 ((((((((x_US_x_A_01C:0.0125396,(((((x_US_x_A_01P:0.00887628,((
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101 x_US_x_A_08P:-0.000190918,x_US_x_A_11P:0.00313157):0.0106883,
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102 x_US_x_A_14C:0.0103815):0.00311658):0.00120812,x_US_x_A_09P:0.00320468):
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103 0.0108828,x_US_x_A_12P:0.00732672):0.00596663,x_US_x_A_07C:0.00449846):0
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104 .00639319,((((x_US_x_A_02P:-2.62303e-05,x_US_x_A_05P:0.00591507):0.
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105 000156788,x_US_x_A_04P:0.00576826):0.00907366,((x_US_x_A_03P:0.00941548,
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106 x_US_x_A_14P:0.00866127):0.00229499,x_US_x_A_13P:0.0209192):0.00469629):
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107 0.0146758,(x_US_x_A_10P:0.000156443,x_US_x_A_15P:0.00578946):0.00472532)
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108 :0.0103079):0.00733948):0.00228489,x_US_x_A_06P:0.00557974):0.00472981,
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109 x_US_x_A_04C:0.00478858):0.00105548,x_US_x_A_05C:0.0120259):0.0060905,
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110 x_US_x_A_12C:0.002911):2.90824e-05,x_US_x_A_11C:-5.79432e-06):4.34574e-
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111 06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538,
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112 x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4.
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113 34574e-06,x_US_x_A_15C:-4.34574e-06);
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114
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115 Which can be partitioned into two groups of leaves, those that end in "P", and those that
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116 end in "C"
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117
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118 1. Reg-exp 1: `P^`
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119 2. Reg-exp 2: `C^`
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120
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121
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122 Output
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123 ------
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124
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125 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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126
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127 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/Slatkin for an example)
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128
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129 Further reading
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130 ---------------
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131
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132 https://github.com/veg/hyphy-analyses/tree/master/SlatkinMaddison
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133
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134
0
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135 ]]></help>
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136 <expand macro="citations">
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137 <citation type="bibtex">
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138 @PUBLISHED{slatkin,
0
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139 author = "Slatkin M, Maddison WP",
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140 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
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141 year = "1989",
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142 note = "Genetics 123(3):603-613",
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143 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
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144 </citation>
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145 </expand>
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146 </tool>