# HG changeset patch
# User iuc
# Date 1567726299 14400
# Node ID 77af4d28aca36e1c8f25177bd5abad7878b29897
# Parent  47c0cf039aae44aa08dcc5de60455f57ba77760d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"

diff -r 47c0cf039aae -r 77af4d28aca3 samtools_fixmate.xml
--- a/samtools_fixmate.xml	Fri Sep 28 04:28:03 2018 -0400
+++ b/samtools_fixmate.xml	Thu Sep 05 19:31:39 2019 -0400
@@ -11,7 +11,7 @@
         ## name sort input 
         #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
             samtools sort
-            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
             -n 
             -O BAM
             -o namesorted.bam