# HG changeset patch
# User iuc
# Date 1580100163 0
# Node ID 44c91703f6a5ce01c05d52bd396b20d386a94fca
# Parent  bc4ada69b61fa1eea9f589d4559a3f48af27f7b8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 9b894593cf3c0156faf679300ded731e0796f792"

diff -r bc4ada69b61f -r 44c91703f6a5 htseq-count.xml
--- a/htseq-count.xml	Thu Oct 10 04:05:45 2019 -0400
+++ b/htseq-count.xml	Mon Jan 27 04:42:43 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="htseq_count" name="htseq-count" version="0.9.1" profile="16.04">
+<tool id="htseq_count" name="htseq-count" version="0.9.1+galaxy1" profile="16.04">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <requirements>
         <requirement type="package" version="0.9.1">htseq</requirement>
@@ -49,7 +49,7 @@
         --secondary-alignments=${advanced_options.secondary_alignments}
         --supplementary-alignments=${advanced_options.supplementary_alignments}
         #if $advanced_options.samout_conditional.samout == "Yes":
-            --samout='$__new_file_path__/${samoutfile.id}_tmp.sam'
+            --samout=samout.sam
         #end if
     #end if
 
@@ -65,7 +65,7 @@
         #if $advanced_options.samout_conditional.samout == "Yes":
             && samtools view -Su
                 -t '${reference_fasta_filename}.fai'
-                '$__new_file_path__/${samoutfile.id}_tmp.sam'
+                samout.sam
             | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' -
         #end if
     #end if