Mercurial > repos > stephenshank > hyphy_fade

annotate hyphy_fade.xml @ 2:a1c92abb3c2f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6e7f074d80e0f35516e223b76e73f019ad45dd74-dirty
author stephenshank
date Wed, 06 Mar 2019 14:27:47 -0500
parents 8f04e527e3ac
children
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bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
parents:
diff changeset
1 <?xml version="1.0"?>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
parents:
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2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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3 <description>: FUBAR* Approach to Directional Evolution (*Fast
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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4 Unconstrained Bayesian Approximation)</description>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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5 <macros>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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6 <import>macros.xml</import>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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7 </macros>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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8 <expand macro="requirements"/>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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9 <version_command>HYPHYMP --version | tail -n 1 | awk '{print
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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10 $1}'</version_command>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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11 <command detect_errors="exit_code"><![CDATA[
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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12 #if $posteriorEstimationMethod == 3:
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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13 ln -s '$input_file' fade_input.fa &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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14 ln -s '$input_nhx' fade_input.nhx &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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15 echo `pwd`/fade_input.fa >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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16 echo `pwd`/fade_input.nhx >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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17 echo '$branches' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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18 echo '$grid_points' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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19 echo '$substitutionmodel' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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20 echo '$posteriorEstimationMethod' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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21 echo '$concentration' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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22 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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23 #else:
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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24 ln -s '$input_file' fade_input.fa &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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25 ln -s '$input_nhx' fade_input.nhx &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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26 echo `pwd`/fade_input.fa >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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27 echo `pwd`/fade_input.nhx >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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28 echo '$branches' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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29 echo '$grid_points' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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30 echo '$substitutionmodel' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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31 echo '$posteriorEstimationMethod' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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32 echo '$mcmc' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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33 echo '$chain_length' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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34 echo '$samples' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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35 echo '$samples_per_chain' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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36 echo '$concentration' >> tool_params &&
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
stephenshank
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37 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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38 #end if
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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39 ]]></command>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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40 <inputs>
1
8f04e527e3ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
stephenshank
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41 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
8f04e527e3ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
stephenshank
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42 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
0
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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43 <param name="branches" type="select" label="Set of branches to test">
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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44 <option value="1">All branches</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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45 <option value="2">Internal branches</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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46 <option value="3">Leaf branches</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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47 <option value="4">Unlabeled branches</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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48 </param>
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49 <param name="substitutionmodel" type="select" label="Substitution Model">
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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50 <option value="1">LG (Generalist empirical model from Le and
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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51 Gascuel 2008)</option>
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52 <option value="2">WAG (Generalist empirical model from Whelon
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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53 and Goldman 2001)</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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54 <option value="3">JTT (Generalist empirical model from Jones,
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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55 Taylor and Thornton 1996)</option>
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56 <option value="4">JC69 (Generalist empirical model with equal
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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57 exhangeability rates among all amino acids)</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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58 <option value="5">mtMet (Specialist empirical model for
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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59 metazoan mitochondrial genomes from Le, Dang and Le
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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60 2007)</option>
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61 <option value="6">mtVer (Specialist empirical model for
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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62 vertebrate mitochondrial gemones from Le, Dang and Le
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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63 2007)</option>
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64 <option value="7">mtInv (Specialist empirical model for
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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65 invertebrate mitochondrial genomes from Le, Dang and Le
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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66 2007)</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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67 <option value="8">gcpREV (Specialist empirical model for
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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68 green plant chloroplast genomes from Cox and Foster
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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69 20013)</option>
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70 <option value="9">HIVBm (Specialist empirical model for
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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71 between-host HIV sequences from Nickle et al. 2007)</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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72 <option value="10">HIVWm (Specialist empirical model for
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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73 within-host HIV sequences from Nickle et al. 2007)</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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74 <option value="11">GTR (General time reversible model; 189
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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75 estimated parameters)</option>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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76 </param>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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77 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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78 <param name="mcmc" type="integer" value="5" min="2" max="20" label="Number of MCMC chains"/>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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79 <param name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain"/>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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80 <param name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in"/>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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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"/>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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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"/>
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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83 <param name="branches" type="select" label="Set of branches to test">
bab74ad497ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2cbd4393b66118f3c12c5111135fcb9397d0152c-dirty
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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>
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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>
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98 </inputs>
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99 <outputs>
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100 <data name="fade_log" format="txt"/>
1
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101 <data name="fade_output" format="hyphy_json_results" from_work_dir="fade_input.fa.FADE.json"/>
0
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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[
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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.
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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>