Mercurial > repos > rdvelazquez > hyphy_fade

annotate hyphy_fade.xml @ 4:b96e3f08a77e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6d367dd55b32854242783723edb80dd7cf2e5272\n'-dirty
author rdvelazquez
date Mon, 19 Nov 2018 16:49:44 -0500
parents f3bd41eea472
children f2ee2e0bde56
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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
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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">
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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
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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 $1}'</version_command>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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11 <command detect_errors="exit_code"><![CDATA[
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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12 ln -s '$input_file' fade_input.fa &&
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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13 ln -s '$input_nhx' fade_input.nhx &&
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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14 echo `pwd`/fade_input.fa >> tool_params &&
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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15 echo `pwd`/fade_input.nhx >> tool_params &&
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9e5fa270a08a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty
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16 echo '$branches' >> tool_params &&
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bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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17 echo '$grid_points' >> tool_params &&
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f3bd41eea472 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6d367dd55b32854242783723edb80dd7cf2e5272\n'-dirty
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18 echo '$substitutionmodel' >> tool_params &&
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b96e3f08a77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6d367dd55b32854242783723edb80dd7cf2e5272\n'-dirty
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19 echo '$posteriorEstimationMethod' > tool_params &&
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bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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20 echo '$mcmc' >> tool_params &&
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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21 echo '$chain_length' >> tool_params &&
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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22 echo '$samples' >> tool_params &&
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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23 echo '$samples_per_chain' >> tool_params &&
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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24 echo '$concentration' >> tool_params &&
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f3bd41eea472 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6d367dd55b32854242783723edb80dd7cf2e5272\n'-dirty
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25 echo '$branches' >> tool_params &&
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bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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26 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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27 ]]></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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28 <inputs>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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29 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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30 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
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31 <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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32 <option value="1">All 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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33 <option value="2">Internal 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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34 <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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35 <option value="4">Unlabeled 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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36 </param>
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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37 <param name="substitutionmodel" type="select" label="Substitution Model">
bcd72352534f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'8052c8a2be65f327ec2d371b6df0081e0d4674a4\n'-dirty
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38 <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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39 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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40 <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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41 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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42 <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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43 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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44 <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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45 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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46 <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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47 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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48 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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49 <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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50 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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51 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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52 <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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53 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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54 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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55 <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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56 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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57 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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58 <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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59 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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60 <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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61 within-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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62 <option value="11">GTR (General time reversible model; 189
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 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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64 </param>
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65 <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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66 <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
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67 <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/>
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68 <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/>
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 <param name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain"/>
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 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
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 <param name="branches" type="select" label="Set of branches to test">
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="1">All branches</option>
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73 <option value="2">Internal branches</option>
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74 <option value="3">Leaf branches</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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75 <option value="4">Unlabeled branches</option>
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76 </param>
4
b96e3f08a77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6d367dd55b32854242783723edb80dd7cf2e5272\n'-dirty
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77 <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
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78 <option value="1">Metropolis-Hastings - Full
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79 Metropolis-Hastings MCMC algorithm (slowest, original 2013
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80 paper implementation)</option>
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81 <option value="2">Collapsed Gibbs - Collapsed Gibbs sampler
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82 (intermediate speed)</option>
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83 <option value="3">Variational Bayes - 0-th order Variational
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84 Bayes approximations (fastest, recommended default)</option>
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85 </param>
0
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86 </inputs>
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87 <outputs>
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88 <data name="fade_log" format="txt"/>
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89 <data name="fade_output" format="json" from_work_dir="fade_input.fa.FADE.json"/>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
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94 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>
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95 <output name="fade_output" file="fade-out1.json" compare="sim_size"/>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
1
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99 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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100 ]]></help>
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101 <expand macro="citations">
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102 <citation type="doi">10.1093/molbev/msv022</citation>
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103 </expand>
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104 </tool>