# HG changeset patch
# User iuc
# Date 1556884190 14400
# Node ID be967733bf819a4c620c084afee10dda34320587
# Parent  c98b3fa910bf65cce901a4f217ac3c211f9bb9f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088

diff -r c98b3fa910bf -r be967733bf81 macros.xml
--- a/macros.xml	Sun Jul 01 16:11:34 2018 -0400
+++ b/macros.xml	Fri May 03 07:49:50 2019 -0400
@@ -6,7 +6,7 @@
             <yield />
         </requirements>
     </xml>
-    <token name="@VERSION@">2.31.9</token>
+    <token name="@VERSION@">2.31.10</token>
 
     <xml name="citations">
         <citations>
diff -r c98b3fa910bf -r be967733bf81 maker.xml
--- a/maker.xml	Sun Jul 01 16:11:34 2018 -0400
+++ b/maker.xml	Fri May 03 07:49:50 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@.1">
+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
     <description>genome annotation pipeline</description>
     <macros>
         <import>macros.xml</import>
@@ -18,7 +18,7 @@
 
         &&
 
-        sed "s/cpus=/cpus=\${GALAXY_SLOTS:-4}/g" '$ctl' > maker_opts.ctl
+        cp '$ctl' maker_opts.ctl
 
         &&
 
@@ -35,7 +35,7 @@
             export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
         #end if
 
-        maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl
+        mpiexec -n \${GALAXY_SLOTS:-4} maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
 
         &&
 
@@ -192,7 +192,7 @@
 
 #-----External Application Behavior Options
 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
-cpus= # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
+cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
 
 #-----MAKER Behavior Options
 max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage)