Mercurial > repos > iuc > hyphy_fade

annotate hyphy_fade.xml @ 2:f65e8fe7d5b8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:46:01 -0500
parents da4192d32e10
children b959fd359a6b
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6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 <?xml version="1.0"?>
2
f65e8fe7d5b8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1">
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3 <description>: FUBAR* Approach to Directional Evolution (*Fast
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4 Unconstrained Bayesian Approximation)</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 ln -s '$input_file' fade_input.fa &&
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11 ln -s '$input_nhx' fade_input.nhx &&
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f65e8fe7d5b8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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12 hyphy fade
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13 --alignment ./fade_input.fa
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14 --tree ./fade_input.nhx
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15 --branches '$branches'
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16 --model '$model'
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17 --method '$posteriorEstimationMethod'
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18 --grid '$grid_points'
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19 --concentration_parameter '$concentration'
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20 #if $posteriorEstimationMethod != "Metropolis-Hastings"
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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21 --chains '$mcmc'
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22 --chain-length '$chain_length'
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23 --burn-in '$samples'
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24 --samples '$samples_per_chain'
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25 #end if
2
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26 --output '$fade_output'
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27 > '$fade_log'
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28 ]]></command>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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29 <inputs>
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30 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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32 <expand macro="branches"/>
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33 <expand macro="substitution" />
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34 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
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35 <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
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36 <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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37 <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
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39 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
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40 <expand macro="branches"/>
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41 <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
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42 <option value="Variational-Bayes">Metropolis-Hastings - Full
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43 Metropolis-Hastings MCMC algorithm (slowest, original 2013
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44 paper implementation)</option>
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45 <option value="Collapsed-Gibbs">Collapsed Gibbs - Collapsed Gibbs sampler
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46 (intermediate speed)</option>
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47 <option value="Metropolis-Hastings">Variational Bayes - 0-th order Variational
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48 Bayes approximations (fastest, recommended default)</option>
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49 </param>
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50 </inputs>
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51 <outputs>
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52 <data name="fade_log" format="txt"/>
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53 <data name="fade_output" format="hyphy_results.json" />
0
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
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58 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
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59 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 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.
1
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64
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65 See the online documentation_ for more information.
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66
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67 .. _documentation: http://hyphy.org/methods/selection-methods/#fade
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68 ]]></help>
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69 <expand macro="citations">
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70 <citation type="doi">10.1093/molbev/msv022</citation>
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71 </expand>
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72 </tool>