# HG changeset patch
# User iuc
# Date 1570694745 14400
# Node ID bc4ada69b61fa1eea9f589d4559a3f48af27f7b8
# Parent  4dd515072667a72b7b662408ae62de28f76b17f9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 95fe80d08fb14c4c344da4979290e72261e31ae5"

diff -r 4dd515072667 -r bc4ada69b61f htseq-count.xml
--- a/htseq-count.xml	Sun Apr 29 09:52:57 2018 -0400
+++ b/htseq-count.xml	Thu Oct 10 04:05:45 2019 -0400
@@ -32,9 +32,9 @@
     #end if
 
     #if $samfile.extension == 'bam':
-        samtools sort -n --output-fmt=SAM -o '$name_sorted_alignment_filename' '$samfile' &&
+        samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' '$samfile' &&
     #else
-        samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n --output-fmt=SAM -o '$name_sorted_alignment_filename' - &&
+        samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' - &&
     #end if
 
     htseq-count
@@ -66,7 +66,7 @@
             && samtools view -Su
                 -t '${reference_fasta_filename}.fai'
                 '$__new_file_path__/${samoutfile.id}_tmp.sam'
-            | samtools sort -o '$samoutfile' -
+            | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' -
         #end if
     #end if
     ]]>
@@ -128,7 +128,7 @@
                             <when value="cached">
                                 <param name="ref_file" type="select" label="Using reference genome">
                                     <options from_data_table="sam_fa_indexes">
-                                        <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
+                                        <filter type="data_meta" key="dbkey" ref="samfile" column="value"/>
                                     </options>
                                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                                 </param>