Mercurial > repos > rdvelazquez > hyphy_fade

comparison hyphy_fade.xml @ 3:f3bd41eea472 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 16:37:57 -0500
parents 77bd5890fc28
children b96e3f08a77e
comparison
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2:77bd5890fc28 3:f3bd41eea472
13 ln -s '$input_nhx' fade_input.nhx && 13 ln -s '$input_nhx' fade_input.nhx &&
14 echo `pwd`/fade_input.fa >> tool_params && 14 echo `pwd`/fade_input.fa >> tool_params &&
15 echo `pwd`/fade_input.nhx >> tool_params && 15 echo `pwd`/fade_input.nhx >> tool_params &&
16 echo '$branches' >> tool_params && 16 echo '$branches' >> tool_params &&
17 echo '$grid_points' >> tool_params && 17 echo '$grid_points' >> tool_params &&
18 echo '$substitutionmodel' > tool_params && 18 echo '$substitutionmodel' >> tool_params &&
19 echo '$posteriorEstimationMethod' > tool_params && 19 echo '1' &&
20 echo '$mcmc' >> tool_params && 20 echo '$mcmc' >> tool_params &&
21 echo '$chain_length' >> tool_params && 21 echo '$chain_length' >> tool_params &&
22 echo '$samples' >> tool_params && 22 echo '$samples' >> tool_params &&
23 echo '$samples_per_chain' >> tool_params && 23 echo '$samples_per_chain' >> tool_params &&
24 echo '$concentration' >> tool_params && 24 echo '$concentration' >> tool_params &&
25 echo '$branches' >> tool_params &&
25 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log' 26 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
26 ]]></command> 27 ]]></command>
27 <inputs> 28 <inputs>
28 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 29 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
29 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> 30 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
71 <option value="1">All branches</option> 72 <option value="1">All branches</option>
72 <option value="2">Internal branches</option> 73 <option value="2">Internal branches</option>
73 <option value="3">Leaf branches</option> 74 <option value="3">Leaf branches</option>
74 <option value="4">Unlabeled branches</option> 75 <option value="4">Unlabeled branches</option>
75 </param> 76 </param>
76 <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
77 <option value="1">Metropolis-Hastings - Full
78 Metropolis-Hastings MCMC algorithm (slowest, original 2013
79 paper implementation)</option>
80 <option value="2">Collapsed Gibbs - Collapsed Gibbs sampler
81 (intermediate speed)</option>
82 <option value="3">Variational Bayes - 0-th order Variational
83 Bayes approximations (fastest, recommended default)</option>
84 </param>
85 </inputs> 77 </inputs>
86 <outputs> 78 <outputs>
87 <data name="fade_log" format="txt"/> 79 <data name="fade_log" format="txt"/>
88 <data name="fade_output" format="json" from_work_dir="fade_input.fa.FADE.json"/> 80 <data name="fade_output" format="json" from_work_dir="fade_input.fa.FADE.json"/>
89 </outputs> 81 </outputs>