# HG changeset patch
# User iuc
# Date 1581716850 18000
# Node ID e90f16ec592970b1a47eb19db78ecd532dd19361
# Parent  a8b34daec0d9411298e11e7417eb39bbc8735b60
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"

diff -r a8b34daec0d9 -r e90f16ec5929 hyphy_fel.xml
--- a/hyphy_fel.xml	Thu Feb 13 15:04:13 2020 -0500
+++ b/hyphy_fel.xml	Fri Feb 14 16:47:30 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0">
+<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy1">
     <description>Fixed Effects Likelihood</description>
     <macros>
         <import>macros.xml</import>
@@ -8,13 +8,14 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' fel_input.fa &&
         ln -s '$input_nhx' fel_input.nhx &&
-        @HYPHY_INVOCATION@ fel
+        @HYPHYMPI@ fel
             --alignment ./fel_input.fa
             --tree ./fel_input.nhx
             --code '$gencodeid'
             --branches '$branches'
             --srv '$include_srv'
             --pvalue '$p_value'
+            --output '$fel_output'
             > '$fel_log'
     ]]></command>
     <inputs>
@@ -29,7 +30,7 @@
     </inputs>
     <outputs>
         <data name="fel_log" format="txt"/>
-        <data name="fel_output" format="hyphy_results.json" from_work_dir="fel_input.fa.FEL.json"/>
+        <data name="fel_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>
diff -r a8b34daec0d9 -r e90f16ec5929 macros.xml
--- a/macros.xml	Thu Feb 13 15:04:13 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:47:30 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>