# HG changeset patch
# User iuc
# Date 1571293530 14400
# Node ID ff313de5f7f4971dcbc70a20ec88e20defac5f20
# Parent  90944a49ad055043ef4953727a728850d52520fe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"

diff -r 90944a49ad05 -r ff313de5f7f4 samtools_view.xml
--- a/samtools_view.xml	Mon Jul 29 08:50:15 2019 -0400
+++ b/samtools_view.xml	Thu Oct 17 02:25:30 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
@@ -228,7 +228,7 @@
             <when value="cached">
                 <param name="ref" type="select" label="Using reference genome">
                     <options from_data_table="fasta_indexes">
-                        <filter column="1" key="dbkey" ref="input" type="data_meta" />
+                        <filter column="dbkey" key="dbkey" ref="input" type="data_meta" />
                         <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
                     </options>
                 </param>