annotate macros.xml @ 33:212c958f6cee draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:15:54 +0000
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">2.5.36</token>
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4 <xml name="inputs">
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5 <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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6 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
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7 </xml>
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8 <xml name="bio_tools">
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9 <xrefs>
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10 <xref type="bio.tools">HyPhy</xref>
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11 </xrefs>
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12 </xml>
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13 <xml name="substitution">
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14 <param name="model" type="select" label="Substitution model">
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15 <option value="GTR">GTR - General time reversible
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16 model</option>
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17 <option value="LG">LG - Generalist empirical model from
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18 Le and Gascuel (2008)</option>
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19 <option value="HIVBm">HIVBm - Specialist empirical model
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20 for between-host HIV sequences</option>
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21 <option value="HIVWm">HIVWm - Specialist empirical model
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22 for within-host HIV sequences</option>
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23 <option value="WAG">WAG - Generalist empirical model from
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24 Whelan and Goldman (2001)</option>
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25 <option value="JTT">JTT - Generalist empirical model from
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26 Jones, Taylor, and Thornton (1996)</option>
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27 <option value="JC69">JC69 - Generalist empirical model
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28 from with equal exchangeability rates</option>
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29 <option value="mtMet">mtMet - Specialist empirical model
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30 for metazoan mitochondrial genomes</option>
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31 <option value="mtVer">mtVer - Specialist empirical model
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32 for vertebrate mitochondrial genomes</option>
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33 <option value="mtInv">mtInv - Specialist empirical model
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34 for invertebrate mitochondrial genomes</option>
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35 <option value="gcpREV">gcpREV - Specialist empirical
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36 model for green plant chloroplast genomes</option>
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37 </param>
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38 </xml>
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39
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40 <xml name="conditional_posteriorEstimationMethod">
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41 <conditional name="posteriorEstimationMethod">
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42 <param argument="--method" type="select" label="Posterior estimation method">
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43 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
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44 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
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45 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
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46 </param>
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47 <when value="Variational-Bayes">
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48 </when>
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49 <when value="Metropolis-Hastings">
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50 <expand macro="mcmc_options" />
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51 </when>
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52 <when value="Collapsed-Gibbs">
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53 <expand macro="mcmc_options" />
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54 </when>
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55 </conditional>
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56 </xml>
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57
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58 <token name="@posteriorEstimationMethod_cmd@">
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59 #if $posteriorEstimationMethod.method != "Variational-Bayes"
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60 --chains '$posteriorEstimationMethod.chains'
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61 --chain-length '$posteriorEstimationMethod.chain_length'
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62 --burn-in '$posteriorEstimationMethod.samples'
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63 --samples '$posteriorEstimationMethod.samples_per_chain'
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64 #end if
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65 </token>
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66
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67 <xml name="mcmc_options">
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68 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
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69 <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
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70 <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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71 <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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72 </xml>
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73
0
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74 <xml name="gencode">
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75 <param name="gencodeid" type="select" label="Genetic code">
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76 <option value="Universal">Universal code</option>
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77 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
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78 code</option>
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79 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
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80 code</option>
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81 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
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82 Coelenterate mt; Mycloplasma/Spiroplasma</option>
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83 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
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84 DNA code</option>
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85 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
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86 Hexamita Nuclear code</option>
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87 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
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88 code</option>
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89 <option value="Euplotid-Nuclear">Euplotid Nuclear
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90 code</option>
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91 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
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92 code</option>
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93 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
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94 code</option>
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95 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
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96 code</option>
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97 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
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98 code</option>
0
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99 </param>
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100 </xml>
13
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101
26
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102 <xml name="srv">
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103 <conditional name="advanced" label="Advanced options">
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104 <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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105 <option value="defaults">Calculate</option>
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106 <option value="specify">Specify values</option>
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107 </param>
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108 <when value="defaults" />
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109 <when value="specify">
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110 <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" />
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111 <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" />
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112 <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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113 <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" />
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114 <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" />
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115 <param name="save_alternative_model" type="boolean" label="Save alternative model fit" />
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116 </when>
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117 </conditional>
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118 </xml>
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119
0
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120 <xml name="branches">
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121 <conditional name="branch_cond">
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122 <param name="branch_sel" type="select" label="Set of branches to test">
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123 <option value="All">All branches</option>
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124 <option value="Internal">Internal branches</option>
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125 <option value="Leaves">Leaf branches</option>
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126 <option value="'Unlabeled-branches'">Unlabeled branches</option>
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127 <option value="specify">Enter a branch label</option>
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128 </param>
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129 <when value="specify">
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130 <param name="branch_label" type="text" value="Test" optional="false" label="Branch label">
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131 <sanitizer invalid_char="">
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132 <valid initial="default" />
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133 </sanitizer>
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134 </param>
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135 </when>
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136 <when value="All" />
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137 <when value="Internal" />
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138 <when value="Leaves" />
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139 <when value="'Unlabeled-branches'" />
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140 </conditional>
0
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141 </xml>
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142 <xml name="citations">
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143 <citations>
6
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144 <citation type="doi">10.1093/molbev/msz197</citation>
1
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145 <yield/>
0
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146 </citations>
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147 </xml>
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148 <xml name="requirements">
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149 <requirements>
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150 <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
1
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151 <yield/>
0
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152 </requirements>
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153 </xml>
26
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154 <xml name="alternative_model_output">
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155 <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">
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156 <filter>advanced['save_alternative_model']</filter>
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157 </data>
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158 </xml>
33
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159 <xml name="resample">
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160 <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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161 </xml>
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162 <token name="@resample@"><![CDATA[
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163 #if $resample:
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164 --resample $resample
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165 #end if
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166 ]]>
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167 </token>
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168
26
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169 <token name="@INPUT_TREE@"><![CDATA[
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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170 #if $input_nhx:
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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171 --tree input.nhx
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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172 #end if
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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173 ]]>
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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174 </token>
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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175 <token name="@branch_options@"><![CDATA[
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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176 #if $branch_cond.branch_sel == 'specify':
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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177 --branches '$branch_cond.branch_label'
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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178 #else:
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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179 --branches $branch_cond.branch_sel
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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180 #end if
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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181 ]]>
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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182 </token>
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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183 <token name="@advanced_options@"><![CDATA[
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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184 #if $advanced.srv_options == 'specify':
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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185 --grid-size $advanced.grid_size
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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186 --starting-points $advanced.starting_points
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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187 --syn-rates $advanced.syn_rates
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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188 --rates $advanced.rates
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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189 --srv $advanced.srv
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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190 #if $advanced.save_alternative_model:
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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191 --save-fit alternative_model.json
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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192 #end if
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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193 #end if
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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194 ]]></token>
17
0b58ef9e84b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"
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195 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
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196 <token name="@ERRORS@"><![CDATA[
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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197 ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
9
cce7b18495e4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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198 ]]></token>
6
f73435dc282b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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199 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
f73435dc282b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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200 export HYPHY=`which hyphy` &&
f73435dc282b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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201 export HYPHY_PATH=`dirname \$HYPHY` &&
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c78f3d7dd1db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2413d0043c5d263ecfa75ec0f8614e322fb65f99"
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202 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
6
f73435dc282b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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203 <token name="@HYPHY_INVOCATION@"><![CDATA[
f73435dc282b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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204 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
f73435dc282b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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205 ]]></token>
24
9275e81b5590 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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206 <token name="@SYMLINK_FILES@"><![CDATA[
26
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207 #if $input_nhx is not None:
24
9275e81b5590 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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208 ln -s '$input_nhx' input.nhx &&
9275e81b5590 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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209 #end if
26
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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210 ln -s '$input_file' input.$input_file.extension &&
5f2ca10db92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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211 #set $input_file = 'input.%s' % $input_file.extension
24
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212 ]]></token>
1
5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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213 </macros>