Mercurial > repos > rdvelazquez > hyphy_fade

annotate hyphy_fade.xml @ 7:a7305e34418f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:12:14 -0500
parents e445c2dc2cce
children 4377e155b9d1
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bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
rdvelazquez
parents:
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1 <?xml version="1.0"?>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
1
9e5fa270a08a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty
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3 <description>: FUBAR* Approach to Directional Evolution (*Fast
0
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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4 Unconstrained Bayesian Approximation)</description>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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5 <macros>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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6 <import>macros.xml</import>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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7 </macros>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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8 <expand macro="requirements"/>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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9 <version_command>HYPHYMP --version | tail -n 1 | awk '{print
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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10 $1}'</version_command>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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11 <command detect_errors="exit_code"><![CDATA[
6
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
rdvelazquez
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12 #if $posteriorEstimationMethod == 3:
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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13 ln -s '$input_file' fade_input.fa &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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14 ln -s '$input_nhx' fade_input.nhx &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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15 echo `pwd`/fade_input.fa >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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16 echo `pwd`/fade_input.nhx >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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17 echo '$branches' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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18 echo '$grid_points' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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19 echo '$substitutionmodel' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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20 echo '$posteriorEstimationMethod' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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21 echo '$concentration' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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22 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
rdvelazquez
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23 #else:
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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24 ln -s '$input_file' fade_input.fa &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
rdvelazquez
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25 ln -s '$input_nhx' fade_input.nhx &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
rdvelazquez
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26 echo `pwd`/fade_input.fa >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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27 echo `pwd`/fade_input.nhx >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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28 echo '$branches' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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29 echo '$grid_points' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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30 echo '$substitutionmodel' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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31 echo '$posteriorEstimationMethod' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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32 echo '$mcmc' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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33 echo '$chain_length' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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34 echo '$samples' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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35 echo '$samples_per_chain' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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36 echo '$concentration' >> tool_params &&
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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37 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
e445c2dc2cce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'248cab6a5bde14c31b944f3d8dd248c5f3cc9443\n'-dirty
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38 #end if
0
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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39 ]]></command>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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40 <inputs>
7
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41 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
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42 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
1
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43 <param name="branches" type="select" label="Set of branches to test">
9e5fa270a08a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty
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44 <option value="1">All branches</option>
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45 <option value="2">Internal branches</option>
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46 <option value="3">Leaf branches</option>
9e5fa270a08a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty
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47 <option value="4">Unlabeled branches</option>
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48 </param>
0
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49 <param name="substitutionmodel" type="select" label="Substitution Model">
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50 <option value="1">LG (Generalist empirical model from Le and
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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51 Gascuel 2008)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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52 <option value="2">WAG (Generalist empirical model from Whelon
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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53 and Goldman 2001)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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54 <option value="3">JTT (Generalist empirical model from Jones,
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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55 Taylor and Thornton 1996)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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56 <option value="4">JC69 (Generalist empirical model with equal
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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57 exhangeability rates among all amino acids)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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58 <option value="5">mtMet (Specialist empirical model for
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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59 metazoan mitochondrial genomes from Le, Dang and Le
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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60 2007)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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61 <option value="6">mtVer (Specialist empirical model for
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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62 vertebrate mitochondrial gemones from Le, Dang and Le
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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63 2007)</option>
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64 <option value="7">mtInv (Specialist empirical model for
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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65 invertebrate mitochondrial genomes from Le, Dang and Le
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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66 2007)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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67 <option value="8">gcpREV (Specialist empirical model for
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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68 green plant chloroplast genomes from Cox and Foster
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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69 20013)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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70 <option value="9">HIVBm (Specialist empirical model for
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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71 between-host HIV sequences from Nickle et al. 2007)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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72 <option value="10">HIVWm (Specialist empirical model for
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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73 within-host HIV sequences from Nickle et al. 2007)</option>
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74 <option value="11">GTR (General time reversible model; 189
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75 estimated parameters)</option>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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76 </param>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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77 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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78 <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
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79 <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/>
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80 <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/>
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81 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
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82 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
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83 <param name="branches" type="select" label="Set of branches to test">
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84 <option value="1">All branches</option>
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85 <option value="2">Internal branches</option>
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86 <option value="3">Leaf branches</option>
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87 <option value="4">Unlabeled branches</option>
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88 </param>
4
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89 <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
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90 <option value="1">Metropolis-Hastings - Full
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91 Metropolis-Hastings MCMC algorithm (slowest, original 2013
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92 paper implementation)</option>
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93 <option value="2">Collapsed Gibbs - Collapsed Gibbs sampler
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94 (intermediate speed)</option>
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95 <option value="3">Variational Bayes - 0-th order Variational
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96 Bayes approximations (fastest, recommended default)</option>
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97 </param>
0
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98 </inputs>
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99 <outputs>
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100 <data name="fade_log" format="txt"/>
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101 <data name="fade_output" format="hyphy_json_results" from_work_dir="fade_input.fa.FADE.json"/>
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102 </outputs>
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103 <tests>
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104 <test>
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105 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
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106 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
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107 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
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108 </test>
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109 </tests>
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110 <help><![CDATA[
1
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111 FADE (FUBAR Approach to Directional Evolution) uses the same underlying algorithmic advances as impletented in FUBAR to apply Baysian MCMC accounting of parameter uncertiantiy to detect sites evolving under directional evolution in protien alignments.
0
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112 ]]></help>
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113 <expand macro="citations">
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114 <citation type="doi">10.1093/molbev/msv022</citation>
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115 </expand>
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116 </tool>