view bam_parallelism_test.xml @ 10:b90e70fb1ac5 draft

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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="infile" split_mode="to_size" split_size="1" shared_inputs="" merge_outputs="outfile"></parallelism>
	<command>

		ln -s $normal input.bam;
		ln -s $normal.metadata.bam_index input.bam.bai;

		touch $outfile;

		cat $infile;

		echo \$(cat $infile);

		samtools view input.bam \$(cat $infile) | head -n 5 >> $outfile;

	</command>
	<inputs>
		<param type="data" format="bam" name="normal" label="Normal Alignment BAM"/>

		<param type="data" format="txt" name="infile" label="Interval File"/>
	</inputs>
	<outputs>
		<data format="txt" name="outfile"/>
	</outputs>
</tool>