# HG changeset patch
# User iuc
# Date 1567726438 14400
# Node ID f2b321f691e40a757217da3b57bd76813fda326e
# Parent  2ec9fb20bb27370bf57a317788bd0de503e3fe8c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"

diff -r 2ec9fb20bb27 -r f2b321f691e4 samtools_view.xml
--- a/samtools_view.xml	Sun Jul 28 14:51:05 2019 -0400
+++ b/samtools_view.xml	Thu Sep 05 19:33:58 2019 -0400
@@ -120,14 +120,14 @@
         ## then sort the output by coordinate, 
         #if not $input.is_of_type('bam') and $outtype == 'bam':
             && samtools sort
-                -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+                -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
                 -O bam
                 -o 'tmpsam'
                 outfile
                 && mv tmpsam outfile
             #if $adv_output.outputpassing == 'yes':
                 && samtools sort
-                    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+                    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
                     -O bam
                     -o 'tmpsam'
                     inv_outfile