# HG changeset patch
# User iuc
# Date 1584300933 14400
# Node ID 14eb2acf30e3f9334ffbc1b5a9c7127621344bab
# Parent  a4b71be30c3c8e12208de300ba800cc39fa35c24
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 7e554792519972b5988f8e451d7466a62cbbc626"

diff -r a4b71be30c3c -r 14eb2acf30e3 raxml.xml
--- a/raxml.xml	Mon Dec 02 07:52:10 2019 -0500
+++ b/raxml.xml	Sun Mar 15 15:35:33 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1">
+<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy2">
     <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
     <requirements>
         <requirement type="package" version="8.2.4">raxml</requirement>
@@ -6,14 +6,13 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
-#set $slots = $getVar('GALAXY_SLOTS', 1)
-#if $slots == 1:
-    raxmlHPC
-    ## Cannot have -T 1
-#else:
-    raxmlHPC-PTHREADS
-    -T $slots
-#end if
+slots=\${GALAXY_SLOTS:-1};
+if [ "\$slots" == "1" ]; then
+    bin="raxmlHPC";
+else
+    bin="raxmlHPC-PTHREADS -T \$slots";
+fi;
+\$bin
 -s '$infile'
 -n galaxy
 #if $search_model_selector.model_type == 'aminoacid':