changeset 3:1d8b63d18f30 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"

--- a/hyphy_busted.xml	Thu Feb 13 15:00:14 2020 -0500
+++ b/hyphy_busted.xml	Fri Feb 14 16:43:12 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0">
+<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy1">
     <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
     <macros>
         <import>macros.xml</import>
@@ -8,11 +8,12 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' busted_input.fa &&
         ln -s '$input_nhx' busted_input.nhx &&
-        @HYPHY_INVOCATION@ busted
+        hyphy busted
             --alignment ./busted_input.fa
             --tree ./busted_input.nhx
             --code $gencodeid
             --branches '$branches'
+            --output '$busted_output'
             > '$busted_log'
         ]]></command>
     <inputs>
@@ -22,7 +23,7 @@
     </inputs>
     <outputs>
         <data name="busted_log" format="txt"/>
-        <data name="busted_output" format="hyphy_results.json" from_work_dir="busted_input.fa.BUSTED.json"/>
+        <data name="busted_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>

--- a/macros.xml	Thu Feb 13 15:00:14 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:43:12 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>