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author marcoalbuquerque
date Mon, 02 Mar 2015 20:06:12 -0500
parents 0ec6a49b43df
children ef32d9b9ba95
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<tool id="bam_parallelism_test" name="BAM Parallelism Test" version="2.4.1">
	<description>
		BAM Parallelism Test
	</description>
	<parallelism method="multi" split_inputs="interval" split_mode="by_rname" real_split="False" merge_outputs="output"/>
	<command>

		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="txt" name="interval" label="Interval File"/>
	</inputs>
	<outputs>
		<data format="txt" name="output"/>
	</outputs>
</tool>