Mercurial > repos > iuc > hyphy_conv

annotate macros.xml @ 12:71ef72fc6dc4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:43:38 +0000
parents 1fc726fccf7c
children
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">2.5.83</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">24.0</token>
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6 <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token>
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7
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8 <xml name="inputs">
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9 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="An in-frame codon alignment in one of the formats supported by HyPhy" />
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10 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file; this will override any trees included in the file" help="A phylogenetic tree (optionally annotated with {})"/>
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11 </xml>
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12 <xml name="bio_tools">
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13 <xrefs>
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14 <xref type="bio.tools">HyPhy</xref>
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15 </xrefs>
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16 </xml>
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17 <xml name="substitution" tokens="argument">
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18 <param argument="@ARGUMENT@" type="select" label="Substitution model">
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19 <option value="LG">LG - Generalist empirical model from
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20 Le and Gascuel (2008)</option>
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21 <option value="WAG">WAG - Generalist empirical model from
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22 Whelan and Goldman (2001)</option>
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23 <option value="JTT" selected="true">JTT - Generalist empirical model from
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24 Jones, Taylor, and Thornton (1996)</option>
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25 <option value="JC69">JC69 - Generalist empirical model
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26 from with equal exchangeability rates</option>
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27 <option value="mtMet">mtMet - Specialist empirical model
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28 for metazoan mitochondrial genomes</option>
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29 <option value="mtVer">mtVer - Specialist empirical model
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30 for vertebrate mitochondrial genomes</option>
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31 <option value="mtInv">mtInv - Specialist empirical model
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32 for invertebrate mitochondrial genomes</option>
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33 <option value="gcpREV">gcpREV - Specialist empirical
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34 model for green plant chloroplast genomes</option>
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35 <option value="HIVBm">HIVBm - Specialist empirical model
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36 for between-host HIV sequences</option>
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37 <option value="HIVWm">HIVWm - Specialist empirical model
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38 for within-host HIV sequences</option>
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39 <option value="GTR" selected="true">GTR - General time reversible
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40 model</option>
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41 </param>
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42 </xml>
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43
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44 <xml name="conditional_posteriorEstimationMethod">
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45 <conditional name="posteriorEstimationMethod">
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46 <param argument="--method" type="select" label="Posterior estimation method" help="The inference method to use for estimating the posterior distribution.">
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47 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
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48 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
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49 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
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50 </param>
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51 <when value="Variational-Bayes">
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52 </when>
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53 <when value="Metropolis-Hastings">
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54 <expand macro="mcmc_options" />
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55 </when>
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56 <when value="Collapsed-Gibbs">
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57 <expand macro="mcmc_options" />
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58 </when>
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59 </conditional>
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60 </xml>
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61
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62 <token name="@posteriorEstimationMethod_cmd@">
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63 #if $posteriorEstimationMethod.method != "Variational-Bayes"
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64 --chains '$posteriorEstimationMethod.chains'
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65 --chain-length '$posteriorEstimationMethod.chain_length'
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66 --burn-in '$posteriorEstimationMethod.samples'
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67 --samples '$posteriorEstimationMethod.samples_per_chain'
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68 #end if
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69 </token>
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70
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71 <xml name="mcmc_options">
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72 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" help="The number of MCMC chains to run." />
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73 <param argument="--chain-length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" help="The length of each MCMC chain." />
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74 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" help="The number of samples to discard from the beginning of each MCMC chain." />
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75 <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" help="The number of samples to draw from each MCMC chain after the burn-in period." />
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76 </xml>
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77
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78 <xml name="gencode">
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79 <param argument="--code" name="gencodeid" type="select" label="Genetic code" help="Which genetic code should be used">
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80 <option value="Universal">Universal code</option>
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81 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
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82 code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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83 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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84 code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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85 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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86 Coelenterate mt; Mycloplasma/Spiroplasma</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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87 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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88 DNA code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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89 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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90 Hexamita Nuclear code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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91 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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92 code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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93 <option value="Euplotid-Nuclear">Euplotid Nuclear
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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94 code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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95 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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96 code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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97 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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98 code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
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99 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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100 code</option>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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101 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
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102 code</option>
12
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103 <option value="Chlorophycean-mtDNA">Chlorophycean-mtDNA</option>
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104 <option value="Trematode-mtDNA">Trematode-mtDNA</option>
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105 <option value="Scenedesmus-obliquus-mtDNA">Scenedesmus-obliquus-mtDNA</option>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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106 <option value="Thraustochytrium-mtDNA">Thraustochytrium-mtDNA</option>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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107 <option value="Pterobranchia-mtDNA">Pterobranchia-mtDNA</option>
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108 <option value="SR1-and-Gracilibacteria">SR1-and-Gracilibacteria</option>
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109 <option value="Pachysolen-Nuclear">Pachysolen-Nuclear</option>
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110 <option value="Mesodinium-Nuclear">Mesodinium-Nuclear</option>
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111 <option value="Peritrich-Nuclear">Peritrich-Nuclear</option>
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112 <option value="Cephalodiscidae-mtDNA">Cephalodiscidae-mtDNA</option>
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113 </param>
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114 </xml>
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115
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116 <xml name="kill_zero_lengths_param">
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117 <param argument="--kill-zero-lengths" type="select" label="Kill zero-length branches" help="Automatically delete internal zero-length branches for computational efficiency">
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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118 <option value="Yes" selected="true">Automatically delete internal zero-length branches for computational efficiency (will not affect results otherwise)</option>
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119 <option value="Constrain">Keep zero-length branches, but constrain their values to 0</option>
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120 <option value="No">Keep all branches</option>
0
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121 </param>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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122 </xml>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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123
2
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124 <xml name="srv">
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125 <conditional name="advanced" label="Advanced options">
12
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126 <param name="srv_options" type="select" label="Advanced parameters" help="Use default values or specify advanced parameters">
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127 <option value="defaults">Use defaults</option>
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128 <option value="specify">Specify values</option>
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129 </param>
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130 <when value="defaults" />
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131 <when value="specify">
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132 <param argument="--grid-size" type="integer" value="250" label="Points in the initial distributional guess for likelihood fitting" max="5000"/>
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133 <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" help="The number of initial random guesses to seed rate values optimization" max="1000"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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134 <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Synonymous rate classes" />
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135 <param argument="--rates" type="integer" min="2" max="10" value="3" label="Non-synonymous rate classes" />
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136 <param argument="--srv" type="select" label="Include synonymous rate variation">
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137 <option value="No" selected="true">No</option>
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138 <option value="Yes">Yes</option>
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139 <option value="Branch-site">Branch-site</option>
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140 <option value="HMM">HMM</option>
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141 </param>
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142 </when>
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143 </conditional>
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144 </xml>
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145
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146 <xml name="busted_advanced_options">
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147 <conditional name="advanced" label="Advanced options">
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148 <param name="srv_options" type="select" label="Advanced parameters" help="Use default values or specify advanced parameters">
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149 <option value="defaults">Use defaults</option>
2
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150 <option value="specify">Specify values</option>
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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151 </param>
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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152 <when value="defaults" />
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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153 <when value="specify">
12
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154 <param argument="--grid-size" type="integer" value="250" max="5000" label="Points in the initial distributional guess for likelihood fitting" help="The number of points in the initial distributional guess for likelihood fitting"/>
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155 <param argument="--starting-points" type="integer" value="1" label="Initial random guesses to seed rate values optimization" help="The number of initial random guesses to seed rate values optimization" max="1000"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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156 <param argument="--syn-rates" type="integer" min="1" max="10" value="3" label="Synonymous rate classes" help="The number of synonymous rate classes to include in the model [1-10, default 3]"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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157 <param argument="--rates" type="integer" min="2" max="10" value="3" label="Non-synonymous rate classes" help="The number of non-synonymous rate classes to include in the model [1-10, default 3]"/>
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158 <param argument="--multiple-hits" type="select" label="Multiple hits correction" help="Include support for multiple nucleotide substitutions">
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159 <option value="None">None</option>
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160 <option value="Double">Double</option>
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161 <option value="Double+Triple">Double and Triple</option>
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162 </param>
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163 <param argument="--error-sink" type="boolean" truevalue="Yes" falsevalue="No" label="Include a rate class for misalignment artifacts (experimental)" help="Include a rate class to capture misalignment artifacts" checked="true"/>
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164 <param name="save_alternative_model" type="boolean" label="Save alternative model fit" help="Save BUSTED model fit to this file (default is not to save)"/>
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165 <conditional name="mss">
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166 <param name="enabled" type="select" label="Include support for multiple synonymous rate class substitutions">
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167 <option value="false" selected="true">No</option>
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168 <option value="true">Yes</option>
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169 </param>
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170 <when value="false"/>
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171 <when value="true">
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172 <conditional name="mss_type_cond">
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173 <param name="mss_type" type="select" label="How to partition synonymous codons into classes">
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174 <option value="Full">Each set of codons mapping to the same amino-acid class have a separate substitution rate (Valine == neutral)</option>
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175 <option value="SynREV">Each set of codons mapping to the same amino-acid class have a separate substitution rate (mean = 1)</option>
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176 <option value="SynREV2">Each pair of synonymous codons mapping to the same amino-acid class and separated by a transition have a separate substitution rate (no rate scaling))</option>
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177 <option value="SynREV2g">Each pair of synonymous codons mapping to the same amino-acid class and separated by a transition have a separate substitution rate (Valine == neutral). All between-class synonymous substitutions share a rate.</option>
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178 <option value="SynREVCodon">Each codon pair that is exchangeable gets its own substitution rate (fully estimated, mean = 1)</option>
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179 <option value="Random">Random partition (specify how many classes; largest class = neutral)</option>
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180 <option value="Empirical">Load a TSV file with an empirical rate estimate for each codon pair</option>
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181 <option value="File">Load a TSV partition from file (prompted for neutral class)</option>
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182 <option value="Codon-file">Load a TSV partition for pairs of codons from a file (prompted for neutral class)</option>
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183 </param>
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184 <when value="Full"/>
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185 <when value="SynREV"/>
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186 <when value="SynREV2"/>
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187 <when value="SynREV2g"/>
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188 <when value="SynREVCodon"/>
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189 <when value="Random">
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190 <param name="mss_classes" type="integer" value="2" label="How many codon rate classes"/>
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191 </when>
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192 <when value="Empirical">
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193 <param name="mss_file" type="data" format="tabular" label="File defining empirical rates for each pair of codons"/>
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194 </when>
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195 <when value="File">
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196 <param name="mss_file" type="data" format="tabular" label="File defining the model partition"/>
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197 <param name="mss_neutral" type="text" value="neutral" label="Designation for the neutral substitution rate"/>
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198 </when>
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199 <when value="Codon-file">
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200 <param name="mss_file" type="data" format="tabular" label="File defining the model partition for pairs of codons"/>
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201 <param name="mss_neutral" type="text" value="neutral" label="Designation for the neutral substitution rate"/>
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202 </when>
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203 </conditional>
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204 </when>
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205 </conditional>
2
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206 </when>
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207 </conditional>
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208 </xml>
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209
12
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210 <xml name="alternative_model_output">
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211 <data name="alternative_model" format="nex" from_work_dir="alternative_model.nhx" label="${tool.name} on ${on_string}: Alternative model">
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212 <filter>advanced_options.save_alternative_model == True</filter>
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213 </data>
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214 </xml>
0
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215 <xml name="branches">
2
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216 <conditional name="branch_cond">
12
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217 <param argument="--branches" name="branch_sel" type="select" label="Set of branches to test" help="Branches to test">
2
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218 <option value="All">All branches</option>
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219 <option value="Internal">Internal branches</option>
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220 <option value="Leaves">Leaf branches</option>
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221 <option value="'Unlabeled-branches'">Unlabeled branches</option>
12
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222 <option value="specify">Custom</option>
2
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223 </param>
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224 <when value="specify">
12
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225 <param name="branch_label" type="text" value="Test" optional="false" label="Branch label" help="The label for the branches to be tested. These labels are case-sensitive and must be present in the Newick tree in {label} format.">
2
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226 <sanitizer invalid_char="">
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227 <valid initial="default" />
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228 </sanitizer>
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229 </param>
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230 </when>
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231 <when value="All" />
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232 <when value="Internal" />
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233 <when value="Leaves" />
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234 <when value="'Unlabeled-branches'" />
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235 </conditional>
0
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236 </xml>
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237 <xml name="citations">
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238 <citations>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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239 <citation type="doi">10.1093/molbev/msz197</citation>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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240 <yield/>
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241 </citations>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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242 </xml>
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243 <xml name="requirements">
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244 <requirements>
8
a8d68d943b70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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245 <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
0
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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diff changeset
246 <yield/>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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247 </requirements>
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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diff changeset
248 </xml>
12
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diff changeset
249 <xml name="regex_sanitizer">
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
250 <sanitizer>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
251 <valid initial="string.ascii_letters,string.digits">
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
252 <add value="^"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
253 <add value="$"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
254 <add value="("/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
255 <add value=")"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
256 <add value="|"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
257 <add value="?"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
258 <add value="*"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
259 <add value="+"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
260 <add value="{"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
261 <add value="-"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
262 <add value="}"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
263 <add value="\"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
264 <add value="["/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
265 <add value="]"/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
266 <add value="."/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
267 <add value=","/>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
268 </valid>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
269 </sanitizer>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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diff changeset
270 <validator type="empty_field" />
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
271 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
2
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
272 </xml>
9
afc4cfb22b78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
273 <xml name="resample">
12
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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diff changeset
274 <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. A value of 0 means no resampling is performed. This parameter specifies the maximum number of replicates per site." />
9
afc4cfb22b78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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parents: 8
diff changeset
275 </xml>
afc4cfb22b78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 8
diff changeset
276 <token name="@resample@"><![CDATA[
afc4cfb22b78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
277 #if $resample:
afc4cfb22b78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
278 --resample $resample
afc4cfb22b78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
279 #end if
12
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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diff changeset
280 ]]></token>
9
afc4cfb22b78 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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parents: 8
diff changeset
281
2
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
282 <token name="@INPUT_TREE@"><![CDATA[
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
283 #if $input_nhx:
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
284 --tree input.nhx
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
285 #end if
12
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
286 ]]></token>
2
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
287 <token name="@branch_options@"><![CDATA[
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
288 #if $branch_cond.branch_sel == 'specify':
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
289 --branches '$branch_cond.branch_label'
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
290 #else:
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
291 --branches $branch_cond.branch_sel
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
292 #end if
12
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
293 ]]></token>
2
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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294 <token name="@advanced_options@"><![CDATA[
12
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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diff changeset
295 #if $advanced.srv_options == 'specify':
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
296 --grid-size $advanced.grid_size
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
297 --starting-points $advanced.starting_points
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
298 --syn-rates $advanced.syn_rates
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
299 --rates $advanced.rates
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
300 --srv '$advanced.srv'
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
301 #end if
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
302 ]]></token>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
303 <token name="@busted_advanced_options_command@"><![CDATA[
2
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
304 #if $advanced.srv_options == 'specify':
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
305 --grid-size $advanced.grid_size
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
306 --starting-points $advanced.starting_points
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
307 --syn-rates $advanced.syn_rates
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
308 --rates $advanced.rates
12
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
309 #if $advanced.multiple_hits != 'None':
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
310 --multiple-hits $advanced.multiple_hits
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
311 #end if
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
312 #if $advanced.error_sink:
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
313 --error-sink Yes
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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parents: 11
diff changeset
314 #end if
2
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents: 0
diff changeset
315 #if $advanced.save_alternative_model:
11
1fc726fccf7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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parents: 9
diff changeset
316 --save-fit alternative_model.nhx
2
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 0
diff changeset
317 #end if
12
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
318 #if $advanced.mss.enabled == "true":
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
319 --mss Yes
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
320 --mss-type $advanced.mss.mss_type_cond.mss_type
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
321 #if $advanced.mss.mss_type_cond.mss_type == "Random":
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
322 --mss-classes $advanced.mss.mss_type_cond.mss_classes
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
323 #elif $advanced.mss.mss_type_cond.mss_type == "Empirical":
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
324 --mss-file $advanced.mss.mss_type_cond.mss_file
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
325 #elif $advanced.mss.mss_type_cond.mss_type == "File":
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
326 --mss-file $advanced.mss.mss_type_cond.mss_file
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
327 --mss-neutral $advanced.mss.mss_type_cond.mss_neutral
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
328 #elif $advanced.mss.mss_type_cond.mss_type == "Codon-file":
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
329 --mss-file $advanced.mss.mss_type_cond.mss_file
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
330 --mss-neutral $advanced.mss.mss_type_cond.mss_neutral
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 11
diff changeset
331 #end if
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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332 #end if
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67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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333 #end if
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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334 ]]></token>
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71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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335 <token name="@srv_options@"><![CDATA[
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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336 #if $srv_conditional.srv_enabled == 'true':
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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337 --srv Yes
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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338 #if $srv_conditional.syn_rates:
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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339 --syn-rates $srv_conditional.syn_rates
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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340 #end if
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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341 #end if
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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342 ]]></token>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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343 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun --allow-run-as-root --oversubscribe -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI </token>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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344 <token name="@HYPHYMP@">hyphy CPU=\${GALAXY_SLOTS:-4} </token>
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67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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345 <token name="@ERRORS@"><![CDATA[
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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346 ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
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6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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347 ]]></token>
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71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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348 <token name="@HYPHY_ENVIRONMENT@">
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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349 export HYPHY=`which hyphy` &amp;&amp;
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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350 export HYPHY_PATH=`dirname \$HYPHY` &amp;&amp;
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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351 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &amp;&amp;</token>
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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352 <token name="@HYPHY_INVOCATION@">
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6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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353 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
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354 </token>
0
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355 <token name="@SYMLINK_FILES@"><![CDATA[
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67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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356 #if $input_nhx is not None:
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6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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357 ln -s '$input_nhx' input.nhx &&
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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358 #end if
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67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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359 ln -s '$input_file' input.$input_file.extension &&
67edc6d534c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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360 #set $input_file = 'input.%s' % $input_file.extension
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6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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361 ]]></token>
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71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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362 <token name="@SYMLINK_FILES_NO_TREE@"><![CDATA[
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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363 ln -s '$input_file' input.$input_file.extension &&
71ef72fc6dc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
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364 ]]></token>
0
6a19eda9b9cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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365 </macros>