# HG changeset patch
# User dpryan79
# Date 1473853998 14400
# Node ID 352e0213806c2f3d9e12033fd73a71a343403c56
# Parent  b55c12d260667121ba927df87471195790aad338
Uploaded

diff -r b55c12d26066 -r 352e0213806c bwameth.xml
--- a/bwameth.xml	Wed Sep 14 07:25:39 2016 -0400
+++ b/bwameth.xml	Wed Sep 14 07:53:18 2016 -0400
@@ -38,7 +38,7 @@
     #else:
         $single_or_paired.input_mate1 $single_or_paired.input_mate2
     #end if
-    | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" output
+    | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" - output
 ]]>
   </command>
   <inputs>
@@ -83,11 +83,11 @@
   <tests>
     <test>
       <param name="referenceSource" value="history" />
-      <param name="reference" value="ref.fa" />
+      <param name="reference" value="ref.fa.gz" />
       <param name="single_or_paired_opts" value="paired" />
       <param name="input_mate1" value="t_R1.fastq.gz" />
       <param name="input_mate2" value="t_R2.fastq.gz" />
-      <output file="output.bam" ftype="bam" name="output" compare="sim_size" delta="10000"/>
+      <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
     </test>
   </tests>
   <help>