Mercurial > repos > rdvelazquez > hyphy_fade

changeset 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
files hyphy_fade.xml
diffstat 1 files changed, 10 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/hyphy_fade.xml	Mon Nov 19 16:37:57 2018 -0500
+++ b/hyphy_fade.xml	Mon Nov 19 16:49:44 2018 -0500
@@ -16,7 +16,7 @@
     echo '$branches' >> tool_params &&
     echo '$grid_points' >> tool_params &&
     echo '$substitutionmodel' >> tool_params &&
-    echo '1' &&
+    echo '$posteriorEstimationMethod' > tool_params &&
     echo '$mcmc' >> tool_params &&
     echo '$chain_length' >> tool_params &&
     echo '$samples' >> tool_params &&
@@ -74,6 +74,15 @@
       <option value="3">Leaf branches</option>
       <option value="4">Unlabeled branches</option>
     </param>
+    <param name="posteriorEstimationMethod" type="select" label="Posterior estimation method">
+      <option value="1">Metropolis-Hastings - Full
+      Metropolis-Hastings MCMC algorithm (slowest, original 2013
+      paper implementation)</option>
+      <option value="2">Collapsed Gibbs - Collapsed Gibbs sampler
+      (intermediate speed)</option>
+      <option value="3">Variational Bayes - 0-th order Variational
+      Bayes approximations (fastest, recommended default)</option>
+    </param>
   </inputs>
   <outputs>
     <data name="fade_log" format="txt"/>