Mercurial > repos > iuc > hyphy_gard

changeset 2:728d5b0af60f 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 16:43:58 -0500
parents a03d87763f51
children bff9a82d630d
files hyphy_gard.xml macros.xml
diffstat 2 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/hyphy_gard.xml	Thu Feb 13 15:00:59 2020 -0500
+++ b/hyphy_gard.xml	Fri Feb 14 16:43:58 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0">
+<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy1">
     <description>Genetic Algorithm for Recombination Detection</description>
     <macros>
         <import>macros.xml</import>
@@ -7,7 +7,7 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' gard_input.fa &&
-        @HYPHY_INVOCATION@ gard
+        @HYPHYMPI@ gard
             --alignment ./gard_input.fa
             --type '$datatype.value'
             #if str($datatype.value) == 'Codon':
--- a/macros.xml	Thu Feb 13 15:00:59 2020 -0500
+++ b/macros.xml	Fri Feb 14 16:43:58 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>