Mercurial > repos > marcoalbuquerque > bam_parallelism_test

changeset 2:6ec7c93b90a6 draft

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Uploaded
author marcoalbuquerque
date Mon, 02 Mar 2015 19:38:47 -0500
parents 213289565e12
children a26d456c51dd
files bam_parallelism_test.xml
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/bam_parallelism_test.xml	Sat Feb 28 19:35:41 2015 -0500
+++ b/bam_parallelism_test.xml	Mon Mar 02 19:38:47 2015 -0500
@@ -2,17 +2,19 @@
 	<description>
 		BAM Parallelism Test
 	</description>
-	<parallelism method="multi" split_inputs="normal,tumour" split_mode="by_rname" real_split="False" merge_outputs="output"/>
+	<parallelism method="multi" split_inputs="interval" split_mode="by_rname" real_split="False" merge_outputs="output"/>
 	<command>
 
-		cat interval.txt;
+		samtools view $normal \$(cat $interval) | head -n 5 > $output;
+		samtools view $tumour \$(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="bed" name="interval" label="Interval File"/>
 	</inputs>
 	<outputs>
-		<data format="bam" name="output"/>
+		<data format="txt" name="output"/>
 	</outputs>
 </tool>
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