# HG changeset patch
# User iuc
# Date 1567726270 14400
# Node ID af994f4458bc0b2b7631bd2bcb5eb374a73e25b3
# Parent  a5429e2e18e8bb97c35c59f966a4748c14486973
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"

diff -r a5429e2e18e8 -r af994f4458bc samtools_fastx.xml
--- a/samtools_fastx.xml	Fri Sep 28 04:38:55 2018 -0400
+++ b/samtools_fastx.xml	Thu Sep 05 19:31:10 2019 -0400
@@ -10,7 +10,7 @@
 @ADDTHREADS@ 
 ## name sort input file if neccessary
 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
-    samtools sort -@ \$addthreads -n '$input' > input &&
+    samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
 #else:
     ln -s '$input' input &&
 #end if