Mercurial > repos > iuc > hyphy_slac

annotate macros.xml @ 35:2753a5c7597a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:16:14 +0000
parents 365e33adf3a4
children
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9da003917dcb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">2.5.47</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">21.05</token>
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6
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7 <xml name="inputs">
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8 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
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9 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
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10 </xml>
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11 <xml name="bio_tools">
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12 <xrefs>
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13 <xref type="bio.tools">HyPhy</xref>
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14 </xrefs>
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15 </xml>
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16 <xml name="substitution" tokens="argument">
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17 <param argument="@ARGUMENT@" type="select" label="Substitution model">
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18 <option value="GTR">GTR - General time reversible
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19 model</option>
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20 <option value="LG">LG - Generalist empirical model from
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21 Le and Gascuel (2008)</option>
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22 <option value="HIVBm">HIVBm - Specialist empirical model
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23 for between-host HIV sequences</option>
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24 <option value="HIVWm">HIVWm - Specialist empirical model
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25 for within-host HIV sequences</option>
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26 <option value="WAG">WAG - Generalist empirical model from
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27 Whelan and Goldman (2001)</option>
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28 <option value="JTT">JTT - Generalist empirical model from
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29 Jones, Taylor, and Thornton (1996)</option>
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30 <option value="JC69">JC69 - Generalist empirical model
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31 from with equal exchangeability rates</option>
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32 <option value="mtMet">mtMet - Specialist empirical model
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33 for metazoan mitochondrial genomes</option>
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34 <option value="mtVer">mtVer - Specialist empirical model
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35 for vertebrate mitochondrial genomes</option>
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36 <option value="mtInv">mtInv - Specialist empirical model
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37 for invertebrate mitochondrial genomes</option>
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38 <option value="gcpREV">gcpREV - Specialist empirical
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39 model for green plant chloroplast genomes</option>
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40 </param>
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41 </xml>
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43 <xml name="conditional_posteriorEstimationMethod">
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44 <conditional name="posteriorEstimationMethod">
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45 <param argument="--method" type="select" label="Posterior estimation method">
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46 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
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47 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
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48 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
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49 </param>
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50 <when value="Variational-Bayes">
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51 </when>
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52 <when value="Metropolis-Hastings">
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53 <expand macro="mcmc_options" />
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54 </when>
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55 <when value="Collapsed-Gibbs">
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56 <expand macro="mcmc_options" />
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57 </when>
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58 </conditional>
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59 </xml>
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60
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61 <token name="@posteriorEstimationMethod_cmd@">
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62 #if $posteriorEstimationMethod.method != "Variational-Bayes"
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63 --chains '$posteriorEstimationMethod.chains'
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64 --chain-length '$posteriorEstimationMethod.chain_length'
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65 --burn-in '$posteriorEstimationMethod.samples'
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66 --samples '$posteriorEstimationMethod.samples_per_chain'
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67 #end if
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68 </token>
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69
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70 <xml name="mcmc_options">
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71 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
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72 <param argument="--chain-length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
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73 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
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74 <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
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75 </xml>
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76
0
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77 <xml name="gencode">
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78 <param argument="--code" name="gencodeid" type="select" label="Genetic code">
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79 <option value="Universal">Universal code</option>
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80 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
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81 code</option>
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82 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
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83 code</option>
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84 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
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85 Coelenterate mt; Mycloplasma/Spiroplasma</option>
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86 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
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87 DNA code</option>
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88 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
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89 Hexamita Nuclear code</option>
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90 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
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91 code</option>
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92 <option value="Euplotid-Nuclear">Euplotid Nuclear
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93 code</option>
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94 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
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95 code</option>
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96 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
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97 code</option>
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98 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
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99 code</option>
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100 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
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101 code</option>
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102 </param>
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103 </xml>
13
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104
26
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105 <xml name="srv">
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106 <conditional name="advanced" label="Advanced options">
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107 <param name="srv_options" type="select" label="Set advanced parameters" help="If these parameters are not set, RELAX will calculate appropriate values at runtime">
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108 <option value="defaults">Calculate</option>
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109 <option value="specify">Specify values</option>
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110 </param>
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111 <when value="defaults" />
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112 <when value="specify">
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113 <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" />
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114 <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" />
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115 <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Alpha rate classes to include in the model" />
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116 <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" />
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117 <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" />
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118 <param name="save_alternative_model" type="boolean" label="Save alternative model fit" />
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119 </when>
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120 </conditional>
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121 </xml>
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122
0
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123 <xml name="branches">
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124 <conditional name="branch_cond">
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125 <param argument="--branches" name="branch_sel" type="select" label="Set of branches to test">
26
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126 <option value="All">All branches</option>
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127 <option value="Internal">Internal branches</option>
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128 <option value="Leaves">Leaf branches</option>
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129 <option value="'Unlabeled-branches'">Unlabeled branches</option>
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130 <option value="specify">Enter a branch label</option>
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131 </param>
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132 <when value="specify">
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133 <param name="branch_label" type="text" value="Test" optional="false" label="Branch label">
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134 <sanitizer invalid_char="">
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135 <valid initial="default" />
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136 </sanitizer>
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137 </param>
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138 </when>
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139 <when value="All" />
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140 <when value="Internal" />
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141 <when value="Leaves" />
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142 <when value="'Unlabeled-branches'" />
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143 </conditional>
0
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144 </xml>
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145 <xml name="citations">
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146 <citations>
6
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147 <citation type="doi">10.1093/molbev/msz197</citation>
1
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148 <yield/>
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149 </citations>
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150 </xml>
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151 <xml name="requirements">
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152 <requirements>
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153 <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
1
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154 <yield/>
0
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155 </requirements>
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156 </xml>
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157 <xml name="alternative_model_output">
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158 <data name="alternative_model" format="nhx" from_work_dir="alternative_model.nhx" label="${tool.name} on ${on_string}: Alternative model">
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159 <filter>advanced['save_alternative_model']</filter>
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160 </data>
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161 </xml>
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162 <xml name="resample">
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163 <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." />
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164 </xml>
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165 <token name="@resample@"><![CDATA[
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166 #if $resample:
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167 --resample $resample
365e33adf3a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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168 #end if
365e33adf3a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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169 ]]>
365e33adf3a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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170 </token>
365e33adf3a4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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171
26
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172 <token name="@INPUT_TREE@"><![CDATA[
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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173 #if $input_nhx:
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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174 --tree input.nhx
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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175 #end if
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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176 ]]>
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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177 </token>
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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178 <token name="@branch_options@"><![CDATA[
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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179 #if $branch_cond.branch_sel == 'specify':
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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180 --branches '$branch_cond.branch_label'
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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181 #else:
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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182 --branches $branch_cond.branch_sel
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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183 #end if
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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184 ]]>
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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185 </token>
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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186 <token name="@advanced_options@"><![CDATA[
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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187 #if $advanced.srv_options == 'specify':
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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188 --grid-size $advanced.grid_size
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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189 --starting-points $advanced.starting_points
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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190 --syn-rates $advanced.syn_rates
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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191 --rates $advanced.rates
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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192 --srv $advanced.srv
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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193 #if $advanced.save_alternative_model:
35
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194 --save-fit alternative_model.nhx
26
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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195 #end if
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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196 #end if
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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197 ]]></token>
17
dc9e52b2d0e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"
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198 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
26
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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199 <token name="@ERRORS@"><![CDATA[
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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200 ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
9
0b4ee5db66ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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201 ]]></token>
6
25782236e47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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202 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
25782236e47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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203 export HYPHY=`which hyphy` &&
25782236e47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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204 export HYPHY_PATH=`dirname \$HYPHY` &&
13
4ddef72f7f21 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2413d0043c5d263ecfa75ec0f8614e322fb65f99"
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205 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
6
25782236e47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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206 <token name="@HYPHY_INVOCATION@"><![CDATA[
25782236e47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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207 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
25782236e47e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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208 ]]></token>
24
ec499ddce7a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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209 <token name="@SYMLINK_FILES@"><![CDATA[
26
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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210 #if $input_nhx is not None:
24
ec499ddce7a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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211 ln -s '$input_nhx' input.nhx &&
ec499ddce7a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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212 #end if
26
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213 ln -s '$input_file' input.$input_file.extension &&
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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214 #set $input_file = 'input.%s' % $input_file.extension
24
ec499ddce7a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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215 ]]></token>
1
c2bed8cc8fc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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216 </macros>