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changeset 0:ab54013c8203 draft

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Uploaded
author marcoalbuquerque
date Sat, 28 Feb 2015 19:29:43 -0500
parents
children 213289565e12
files bam_parallelism_test.xml
diffstat 1 files changed, 22 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_parallelism_test.xml	Sat Feb 28 19:29:43 2015 -0500
@@ -0,0 +1,22 @@
+<tool id="bam_parallelism_test" name="BAM Parallelism Test" version="2.4.1">
+	<description>
+		BAM Parallelism Test
+	</description>
+	<parallelism method="multi" split_inputs="normal,tumour" split_mode="by_rname" real_split="False" merge_outputs="output"/>
+	<command>
+
+		{
+		samtools view -H $normal;
+		samtools view $normal \$(echo interval.txt) | head -n5;
+		samtools view $tumour \$(echo interval.txt) | head -n5;
+		} | samtools view -bS - > $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"/>
+	</inputs>
+	<outputs>
+		<data format="bam" name="output"/>
+	</outputs>
+</tool>
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