# HG changeset patch
# User eduardo
# Date 1438700391 14400
# Node ID e0e38389a9cbe918842f2a0f548411731f97241a
# Parent  8f36fc7279881195ae628ede8b4b45dd033b99bd
Uploaded

diff -r 8f36fc727988 -r e0e38389a9cb download_align.xml
--- a/download_align.xml	Tue Aug 04 09:46:15 2015 -0400
+++ b/download_align.xml	Tue Aug 04 10:59:51 2015 -0400
@@ -14,10 +14,10 @@
   #else:
     #set index_path = $reference_genome.index.fields.path
   #end if
-  wget -O - $file | gunzip -c | cutadapt   -q 20 - | bowtie2  -q 
+  wget -O - $file | gunzip -c | cutadapt   -q 20 -m 20 - | bowtie2  -q 
   ## index file path
   -x $index_path 
-  -U - | samtools view -b - > $output
+  -U - | samtools view -bS - > $output
   </command>
   <stdio>
     <exit_code range="1:" level="fatal" description="Tool exception" />