Mercurial > repos > rdvelazquez > hyphy_fade
comparison hyphy_fade.xml @ 2:77bd5890fc28 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty
author | rdvelazquez |
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date | Mon, 19 Nov 2018 14:25:34 -0500 |
parents | 9e5fa270a08a |
children | f3bd41eea472 |
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1:9e5fa270a08a | 2:77bd5890fc28 |
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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 '$posteriorEstimationMethod' > tool_params && | |
19 echo '$mcmc' >> tool_params && | 20 echo '$mcmc' >> tool_params && |
20 echo '$chain_length' >> tool_params && | 21 echo '$chain_length' >> tool_params && |
21 echo '$samples' >> tool_params && | 22 echo '$samples' >> tool_params && |
22 echo '$samples_per_chain' >> tool_params && | 23 echo '$samples_per_chain' >> tool_params && |
23 echo '$concentration' >> tool_params && | 24 echo '$concentration' >> tool_params && |
24 echo '$branches' >> tool_params && | |
25 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log' | 25 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log' |
26 ]]></command> | 26 ]]></command> |
27 <inputs> | 27 <inputs> |
28 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> | 28 <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"/> | 29 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> |
71 <option value="1">All branches</option> | 71 <option value="1">All branches</option> |
72 <option value="2">Internal branches</option> | 72 <option value="2">Internal branches</option> |
73 <option value="3">Leaf branches</option> | 73 <option value="3">Leaf branches</option> |
74 <option value="4">Unlabeled branches</option> | 74 <option value="4">Unlabeled branches</option> |
75 </param> | 75 </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> | |
76 </inputs> | 85 </inputs> |
77 <outputs> | 86 <outputs> |
78 <data name="fade_log" format="txt"/> | 87 <data name="fade_log" format="txt"/> |
79 <data name="fade_output" format="json" from_work_dir="fade_input.fa.FADE.json"/> | 88 <data name="fade_output" format="json" from_work_dir="fade_input.fa.FADE.json"/> |
80 </outputs> | 89 </outputs> |