# HG changeset patch
# User marcoalbuquerque
# Date 1425344635 18000
# Node ID 0ec6a49b43df35c865fd2b980f6da7fb7e3bf217
# Parent  a26d456c51ddfeb497e3691461b8889db10ab6c5
Uploaded

diff -r a26d456c51dd -r 0ec6a49b43df bam_parallelism_test.xml
--- a/bam_parallelism_test.xml	Mon Mar 02 20:01:11 2015 -0500
+++ b/bam_parallelism_test.xml	Mon Mar 02 20:03:55 2015 -0500
@@ -5,13 +5,15 @@
 	<parallelism method="multi" split_inputs="interval" split_mode="by_rname" real_split="False" merge_outputs="output"/>
 	<command>
 
-		samtools view $normal \$(cat $interval) | head -n 5 > $output;
-		samtools view $tumour \$(cat $interval) | head -n 5 >> $output;
+		ln -s $normal input.bam
+		ln -s $normal.metadata.bam_index input.bam.bai
+
+		samtools view input.bam \$(cat $interval) | head -n 5 > $output;
 
 	</command>
 	<inputs>
 		<param type="data" format="bam" name="normal" label="Normal Alignment BAM"/>
-		<param type="data" format="bam" name="tumour" label="Tumour Alignment BAM"/>
+
 		<param type="data" format="txt" name="interval" label="Interval File"/>
 	</inputs>
 	<outputs>