Mercurial > repos > iuc > hyphy_fade

annotate hyphy_fade.xml @ 0:6164d9298db9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:25:26 -0400
parents
children da4192d32e10
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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"?>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 <description>: FUBAR* Approach to Directional Evolution (*Fast
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 Unconstrained Bayesian Approximation)</description>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5 <macros>
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6 <import>macros.xml</import>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 </macros>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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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 '$input_file' fade_input.fa &&
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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11 ln -s '$input_nhx' fade_input.nhx &&
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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12 @HYPHY_INVOCATION@ fade
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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13 --alignment ./fade_input.fa
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 --tree ./fade_input.nhx
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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15 --branches '$branches'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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16 --model '$model'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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17 --method '$posteriorEstimationMethod'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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18 --grid '$grid_points'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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19 --concentration_parameter '$concentration'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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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'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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22 --chain-length '$chain_length'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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23 --burn-in '$samples'
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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24 --samples '$samples_per_chain'
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25 #end if
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26 > '$fade_log'
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27 ]]></command>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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28 <inputs>
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29 <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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30 <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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31 <expand macro="branches"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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32 <expand macro="substitution" />
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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33 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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34 <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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35 <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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36 <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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37 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 <expand macro="branches"/>
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40 <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
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41 <option value="Variational-Bayes">Metropolis-Hastings - Full
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42 Metropolis-Hastings MCMC algorithm (slowest, original 2013
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43 paper implementation)</option>
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44 <option value="Collapsed-Gibbs">Collapsed Gibbs - Collapsed Gibbs sampler
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45 (intermediate speed)</option>
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46 <option value="Metropolis-Hastings">Variational Bayes - 0-th order Variational
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47 Bayes approximations (fastest, recommended default)</option>
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48 </param>
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49 </inputs>
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50 <outputs>
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51 <data name="fade_log" format="txt"/>
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52 <data name="fade_output" format="hyphy_results.json" from_work_dir="fade_input.fa.FADE.json"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
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57 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
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58 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 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.
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63 ]]></help>
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64 <expand macro="citations">
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65 <citation type="doi">10.1093/molbev/msv022</citation>
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66 </expand>
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67 </tool>