Mercurial > repos > rdvelazquez > hyphy_fubar

comparison hyphy_fubar.xml @ 1:fa2236bc5ab2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty
author rdvelazquez
date Sun, 18 Nov 2018 22:58:53 -0500
parents a52fcdeacf3d
children 203597c4875e
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0:a52fcdeacf3d 1:fa2236bc5ab2
8 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> 8 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 ln -s '$input_file' fubar_input.fa && 11 ln -s '$input_file' fubar_input.fa &&
12 ln -s '$input_nhx' fubar_input.nhx && 12 ln -s '$input_nhx' fubar_input.nhx &&
13 echo $gencodeid > fubar_params && 13 echo $gencodeid > tool_params &&
14 echo `pwd`/fubar_input.fa >> fubar_params && 14 echo `pwd`/fubar_input.fa >> tool_params &&
15 echo `pwd`/fubar_input.nhx >> fubar_params && 15 echo `pwd`/fubar_input.nhx >> tool_params &&
16 echo '$grid_points' >> fubar_params && 16 echo '$grid_points' >> tool_params &&
17 echo '$mcmc' >> fubar_params && 17 echo '$mcmc' >> tool_params &&
18 echo '$chain_length' >> fubar_params && 18 echo '$chain_length' >> tool_params &&
19 echo '$samples' >> fubar_params && 19 echo '$samples' >> tool_params &&
20 echo '$samples_per_chain' >> fubar_params && 20 echo '$samples_per_chain' >> tool_params &&
21 echo '$concentration' >> fubar_params && 21 echo '$concentration' >> tool_params &&
22 export HYPHY=`which HYPHYMP` && 22 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf > '$fubar_log'
23 export HYPHY_PATH=`dirname \$HYPHY` &&
24 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&
25 cat fubar_params | HYPHYMP LIBPATH=\$HYPHY_LIB \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf > '$fubar_log'
26 ]]> 23 ]]>
27 </command> 24 </command>
28 <inputs> 25 <inputs>
29 <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> 26 <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
30 <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> 27 <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
65 Model-based selection analyses (such as those performed by PAML and HyPhy) can be slow, becoming impractical for large alignments. We present a method to model and detect selection much faster than existing methods and to leverage Bayesian MCMC to robustly account for parameter estimation errors. 62 Model-based selection analyses (such as those performed by PAML and HyPhy) can be slow, becoming impractical for large alignments. We present a method to model and detect selection much faster than existing methods and to leverage Bayesian MCMC to robustly account for parameter estimation errors.
66 63
67 Results: By exploiting some commonly used approximations, FUBAR can perform detection of positive selection under a model that allows rich site- to-site rate variation about 30 to 50 times faster than existing random effects likelihood methods, and 10 to 30 times faster than existing fixed effects likelihood methods. We introduce an ultra-fast MCMC routine that allows a flexible prior specification, with no parametric constraints on the prior shape. Furthermore, our method allows us to visualize Bayesian inference for each site, revealing the model supported by the data. 64 Results: By exploiting some commonly used approximations, FUBAR can perform detection of positive selection under a model that allows rich site- to-site rate variation about 30 to 50 times faster than existing random effects likelihood methods, and 10 to 30 times faster than existing fixed effects likelihood methods. We introduce an ultra-fast MCMC routine that allows a flexible prior specification, with no parametric constraints on the prior shape. Furthermore, our method allows us to visualize Bayesian inference for each site, revealing the model supported by the data.
68 ]]> 65 ]]>
69 </help> 66 </help>
70 <expand macro="citations" /> 67 <expand macro="citations">
68 <citation type="doi">10.1093/molbev/mst030</citation>
69 </expand>
71 </tool> 70 </tool>