# HG changeset patch
# User iuc
# Date 1567726526 14400
# Node ID 1fc8d53bc352384f2dbe2abca1ddf6ab66d46067
# Parent  739b008acace0d705d10eda998d4b1e62808994d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"

diff -r 739b008acace -r 1fc8d53bc352 bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Fri Aug 23 13:24:01 2019 -0400
+++ b/bowtie2_wrapper.xml	Thu Sep 05 19:35:26 2019 -0400
@@ -305,7 +305,7 @@
 
 ## output file
 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
-    | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
+    | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
 #else if $sam_options.reorder:
     | samtools view -bS - -o '$output'
 #else: