# HG changeset patch
# User rdvelazquez
# Date 1542655534 18000
# Node ID 77bd5890fc2814ca1e865718615e1d17cb04c93e
# Parent  9e5fa270a08a60b1021c779d0218978a2d7c5989
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'bff24ad0eccc4083de076adc029c5c3ac50e2852\n'-dirty

diff -r 9e5fa270a08a -r 77bd5890fc28 hyphy_fade.xml
--- a/hyphy_fade.xml	Sun Nov 18 22:57:28 2018 -0500
+++ b/hyphy_fade.xml	Mon Nov 19 14:25:34 2018 -0500
@@ -15,13 +15,13 @@
     echo `pwd`/fade_input.nhx >> tool_params &&
     echo '$branches' >> tool_params &&
     echo '$grid_points' >> tool_params &&
-    echo $substitutionmodel > tool_params &&
+    echo '$substitutionmodel' > tool_params &&
+    echo '$posteriorEstimationMethod' > tool_params &&
     echo '$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>
@@ -73,6 +73,15 @@
       <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"/>
diff -r 9e5fa270a08a -r 77bd5890fc28 test-data/fade-in1.fa.FADE.cache
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fade-in1.fa.FADE.cache	Mon Nov 19 14:25:34 2018 -0500
@@ -0,0 +1,2 @@
+{
+}
\ No newline at end of file