# HG changeset patch
# User stephenshank
# Date 1547751918 18000
# Node ID bb0068875ac6c144a450149d2cf087b0fa1129e2
# Parent  09b050170437ec69fcc68f6e14307d5b67a6fa5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 74206c79038a0dbd29a5581bf66e08721a4dfda2-dirty

diff -r 09b050170437 -r bb0068875ac6 hyphy_bgm.xml
--- a/hyphy_bgm.xml	Thu Jan 17 09:50:49 2019 -0500
+++ b/hyphy_bgm.xml	Thu Jan 17 14:05:18 2019 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0">
-  <description>: Bayesian Graphical Models</description>
+  <description>- Detecting coevolving sites via Bayesian graphical models</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -18,7 +18,7 @@
       echo '$datatype.model' >> tool_params &&
     #end if
     echo `pwd`/bgm_input.nhx >> tool_params &&
-    echo '1' >> tool_params &&
+    echo '$branch_subset' >> tool_params &&
     echo '$chain_length' >> tool_params &&
     echo '$burn_in' >> tool_params &&
     echo '$sample' >> tool_params &&
@@ -69,6 +69,13 @@
         </param>
       </when>
     </conditional>
+    <param name="branch_subset" type="select" label="Subset of branches to include substitutions from">
+      <option value="1">All</option>
+      <option value="2">Internal</option>
+      <option value="3">Leaves</option>
+      <option value="4">Unlabeled</option>
+      <option value="5">Labeled</option>
+    </param>
     <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
     <param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
     <param name="sample" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>