changeset 3:242ed2357a01 draft

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

--- a/hyphy_slac.xml	Thu Feb 13 15:03:50 2020 -0500
+++ b/hyphy_slac.xml	Fri Feb 14 16:47:07 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0">
+<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1">
     <description>Single Likelihood Ancestor Counting</description>
     <macros>
         <import>macros.xml</import>
@@ -8,13 +8,14 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' slac_input.fa &&
         ln -s '$input_nhx' slac_input.nhx &&
-        @HYPHY_INVOCATION@ slac
+        hyphy slac
             --alignment ./slac_input.fa
             --tree ./slac_input.nhx
             --code '$gencodeid'
             --branches '$branches'
             --samples '$number_of_samples'
             --pvalue '$p_value'
+            --output '$slac_output'
         > '$slac_log'
     ]]></command>
     <inputs>
@@ -26,7 +27,7 @@
     </inputs>
     <outputs>
         <data name="slac_log" format="txt"/>
-        <data name="slac_output" format="hyphy_results.json" from_work_dir="slac_input.fa.SLAC.json"/>
+        <data name="slac_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>

--- a/macros.xml	Thu Feb 13 15:03:50 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:47:07 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>