# HG changeset patch
# User iuc
# Date 1581716616 18000
# Node ID f2c6ada85b41d3d851a02d6dc4ff08f3939d45a1
# Parent  cdfa1afd7cb058b881180fe1b4cf09ef6e6a97be
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"

diff -r cdfa1afd7cb0 -r f2c6ada85b41 hyphy_bgm.xml
--- a/hyphy_bgm.xml	Thu Feb 13 15:00:37 2020 -0500
+++ b/hyphy_bgm.xml	Fri Feb 14 16:43:36 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0">
+<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy1">
     <description>- Detecting coevolving sites via Bayesian graphical models</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' bgm_input.fa &&
         ln -s '$input_nhx' bgm_input.nhx &&
-        @HYPHY_INVOCATION@ bgm
+        hyphy bgm
             --alignment ./bgm_input.fa
             --tree ./bgm_input.nhx
             --run_type $datatype.value
diff -r cdfa1afd7cb0 -r f2c6ada85b41 macros.xml
--- a/macros.xml	Thu Feb 13 15:00:37 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:43:36 2020 -0500
@@ -80,6 +80,7 @@
             <yield/>
         </requirements>
     </xml>
+    <token name="@HYPHYMPI@">mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI</token>
     <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
 export HYPHY_PATH=`dirname \$HYPHY` &&
 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>