Mercurial > repos > rdvelazquez > hyphy_fade

diff 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
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line diff
--- a/hyphy_fade.xml	Mon Nov 19 14:25:34 2018 -0500
+++ b/hyphy_fade.xml	Mon Nov 19 16:37:57 2018 -0500
@@ -15,13 +15,14 @@
     echo `pwd`/fade_input.nhx >> tool_params &&
     echo '$branches' >> tool_params &&
     echo '$grid_points' >> tool_params &&
-    echo '$substitutionmodel' > tool_params &&
-    echo '$posteriorEstimationMethod' > tool_params &&
+    echo '$substitutionmodel' >> tool_params &&
+    echo '1' &&
     echo '$mcmc' >> tool_params &&
     echo '$chain_length' >> tool_params &&
     echo '$samples' >> tool_params &&
     echo '$samples_per_chain' >> tool_params &&
     echo '$concentration' >> tool_params &&
+    echo '$branches' >> tool_params &&
     @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
     ]]></command>
   <inputs>
@@ -73,15 +74,6 @@
       <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"/>