Mercurial > repos > iuc > samtools_view

diff samtools_view.xml @ 5:f2b321f691e4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:33:58 -0400
parents 097c44aaf6d4
children 1e7eb419a5be
line wrap: on
line diff
--- 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