changeset 2:f65e8fe7d5b8 draft

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

--- a/hyphy_fade.xml	Thu Feb 13 15:02:39 2020 -0500
+++ b/hyphy_fade.xml	Fri Feb 14 16:46:01 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
+<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1">
     <description>: FUBAR* Approach to Directional Evolution (*Fast
     Unconstrained Bayesian Approximation)</description>
     <macros>
@@ -9,7 +9,7 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' fade_input.fa &&
         ln -s '$input_nhx' fade_input.nhx &&
-        @HYPHY_INVOCATION@ fade
+        hyphy fade
             --alignment ./fade_input.fa
             --tree ./fade_input.nhx
             --branches '$branches'
@@ -23,6 +23,7 @@
                 --burn-in '$samples'
                 --samples '$samples_per_chain'
             #end if
+            --output '$fade_output'
             > '$fade_log'
     ]]></command>
     <inputs>
@@ -49,7 +50,7 @@
     </inputs>
     <outputs>
         <data name="fade_log" format="txt"/>
-        <data name="fade_output" format="hyphy_results.json" from_work_dir="fade_input.fa.FADE.json"/>
+        <data name="fade_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>

--- a/macros.xml	Thu Feb 13 15:02:39 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:46:01 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>