--- a/stringtie.xml	Fri May 03 11:05:13 2019 -0400
+++ b/stringtie.xml	Tue Feb 25 18:07:47 2020 -0500
@@ -21,11 +21,13 @@
 #end if
 
 #if $input_bam.metadata.ftype == 'sam':
-    samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' | stringtie
+    samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' -T "\${TMPDIR:-.}" | stringtie
 #else
     stringtie '$input_bam'
 #end if
 
+$long_reads
+
 -o '$output_gtf'
 -p "\${GALAXY_SLOTS:-1}"
 
@@ -110,6 +112,7 @@
     ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/>
+        <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Input contains long reads?" help="Select if the input contains long error-prone reads, e.g. from Oxford Nanopore or PacBio sequencing."/>
         <param name="rna_strandness" type="select" label="Specify strand information"
             help="Select 'Forward (FR)' if your reads are from a forward-stranded library, 'Reverse (RF)' if your reads are from a reverse-stranded library, or 'Unstranded' if your reads are not from a stranded library. See Help section below for more information. Default: Unstranded">
                 <option value="" selected="true">Unstranded</option>