Mercurial > repos > iuc > hyphy_absrel

changeset 3:fb40b0928cad draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:44:41 -0500
parents de93e1fbdc31
children 181f5b9f139f
files hyphy_absrel.xml macros.xml
diffstat 2 files changed, 8 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/hyphy_absrel.xml	Thu Feb 13 15:01:22 2020 -0500
+++ b/hyphy_absrel.xml	Fri Feb 14 16:44:41 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
+<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1">
     <description>adaptive Branch Site Random Effects Likelihood</description>
     <macros>
         <import>macros.xml</import>
@@ -8,12 +8,15 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' absrel_input.fa &&
         ln -s '$input_nhx' absrel_input.nhx &&
-        @HYPHY_INVOCATION@ absrel
+        @HYPHYMPI@ absrel
             --alignment ./absrel_input.fa
             --tree ./absrel_input.nhx
             --code '$gencodeid'
             --branches '$branches'
-            > '$absrel_log'
+            --output '$absrel_output'
+            #if $log:
+                > '$absrel_log'
+            #end if
         ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -25,7 +28,7 @@
         <data name="absrel_log" format="txt">
             <filter>log</filter>
         </data>
-        <data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/>
+        <data name="absrel_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>
--- a/macros.xml	Thu Feb 13 15:01:22 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:44:41 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>