Mercurial > repos > iuc > hyphy_sm19

annotate macros.xml @ 24:6d529bf13e2e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e22821f51ae326b3696a9456cbc44f9982512a52"
author iuc
date Tue, 20 Apr 2021 19:50:49 +0000
parents f1261376fd4b
children 36e40d93e8a3
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="inputs">
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4 <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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5 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
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6 </xml>
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7 <xml name="substitution">
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8 <param name="model" type="select" label="Substitution model">
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9 <option value="GTR">GTR - General time reversible
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10 model</option>
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11 <option value="LG">LG - Generalist empirical model from
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12 Le and Gascuel (2008)</option>
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13 <option value="HIVBm">HIVBm - Specialist empirical model
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14 for between-host HIV sequences</option>
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15 <option value="HIVWm">HIVWm - Specialist empirical model
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16 for within-host HIV sequences</option>
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17 <option value="WAG">WAG - Generalist empirical model from
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18 Whelan and Goldman (2001)</option>
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19 <option value="JTT">JTT - Generalist empirical model from
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20 Jones, Taylor, and Thornton (1996)</option>
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21 <option value="JC69">JC69 - Generalist empirical model
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22 from with equal exchangeability rates</option>
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23 <option value="mtMet">mtMet - Specialist empirical model
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24 for metazoan mitochondrial genomes</option>
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25 <option value="mtVer">mtVer - Specialist empirical model
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26 for vertebrate mitochondrial genomes</option>
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27 <option value="mtInv">mtInv - Specialist empirical model
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28 for invertebrate mitochondrial genomes</option>
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29 <option value="gcpREV">gcpREV - Specialist empirical
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30 model for green plant chloroplast genomes</option>
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31 </param>
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32 </xml>
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34 <xml name="conditional_posteriorEstimationMethod">
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35 <conditional name="posteriorEstimationMethod">
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36 <param argument="--method" type="select" label="Posterior estimation method">
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37 <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>
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38 <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>
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39 <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>
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40 </param>
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41 <when value="Variational-Bayes">
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42 </when>
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43 <when value="Metropolis-Hastings">
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44 <expand macro="mcmc_options" />
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45 </when>
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46 <when value="Collapsed-Gibbs">
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47 <expand macro="mcmc_options" />
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48 </when>
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49 </conditional>
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50 </xml>
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51
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52 <token name="@posteriorEstimationMethod_cmd@">
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53 #if $posteriorEstimationMethod.method != "Variational-Bayes"
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54 --chains '$posteriorEstimationMethod.chains'
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55 --chain-length '$posteriorEstimationMethod.chain_length'
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56 --burn-in '$posteriorEstimationMethod.samples'
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57 --samples '$posteriorEstimationMethod.samples_per_chain'
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58 #end if
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59 </token>
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60
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61 <xml name="mcmc_options">
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62 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
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63 <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
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64 <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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65 <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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66 </xml>
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67
0
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68 <xml name="gencode">
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69 <param name="gencodeid" type="select" label="Genetic code">
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70 <option value="Universal">Universal code</option>
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71 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
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72 code</option>
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73 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
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74 code</option>
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75 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
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76 Coelenterate mt; Mycloplasma/Spiroplasma</option>
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77 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
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78 DNA code</option>
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79 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
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80 Hexamita Nuclear code</option>
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81 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
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82 code</option>
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83 <option value="Euplotid-Nuclear">Euplotid Nuclear
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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84 code</option>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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85 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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86 code</option>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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87 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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88 code</option>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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89 <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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90 code</option>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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91 <option value="Blepharisma-Nuclear">Blepharisma Nuclear
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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92 code</option>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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93 </param>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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94 </xml>
12
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95
0
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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96 <xml name="branches">
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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97 <param name="branches" type="select" label="Set of branches to test">
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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98 <option value="All">All branches</option>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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99 <option value="Internal">Internal branches</option>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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100 <option value="Leaves">Leaf branches</option>
5
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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101 <option value="'Unlabeled-branches'">Unlabeled branches</option>
0
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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102 </param>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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103 </xml>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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104 <xml name="citations">
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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105 <citations>
5
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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106 <citation type="doi">10.1093/molbev/msz197</citation>
0
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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107 <yield/>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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108 </citations>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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109 </xml>
23
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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110 <token name="@VERSION@">2.5.31</token>
0
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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111 <xml name="requirements">
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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112 <requirements>
5
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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113 <requirement type="package" version="@VERSION@">hyphy</requirement>
0
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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114 <yield/>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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115 </requirements>
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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116 </xml>
16
2126c9e28ce6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"
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117 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
23
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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118 <token name="@CATCH_ERROR@"><![CDATA[
8
6cf8d753e93e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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119 EC=\$? ;
6cf8d753e93e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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120 if [ \$EC -ne 0 ] ; then
23
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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121 if [ -f errors.log.mpinode0 ] ; then
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122 cat errors.log.mpinode0 >&2 ;
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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123 else
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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124 cat errors.log >&2 ;
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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125 fi ;
8
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126 fi ;
6cf8d753e93e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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127 exit \$EC
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128 ]]></token>
5
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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129 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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130 export HYPHY=`which hyphy` &&
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131 export HYPHY_PATH=`dirname \$HYPHY` &&
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132 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token>
5
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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133 <token name="@HYPHY_INVOCATION@"><![CDATA[
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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134 @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB
5f1830cb9135 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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135 ]]></token>
23
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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136 <token name="@SYMLINK_FILES@"><![CDATA[
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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137 ln -s '$input_file' input.$input_file.extension &&
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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138 ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json &&
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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139 #set $input_file = 'input.%s' % $input_file.extension
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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140 #if $input_nhx:
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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141 ln -s '$input_nhx' input.nhx &&
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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142 #end if
f1261376fd4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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143 ]]></token>
0
ae7c42d49717 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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144 </macros>