Mercurial > repos > marcoalbuquerque > bam_parallelism_test

changeset 9:06f281bbdf5b draft

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Uploaded
author marcoalbuquerque
date Mon, 02 Mar 2015 20:30:00 -0500
parents f7cb864d1b3f
children b90e70fb1ac5
files bam_parallelism_test.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/bam_parallelism_test.xml	Mon Mar 02 20:16:55 2015 -0500
+++ b/bam_parallelism_test.xml	Mon Mar 02 20:30:00 2015 -0500
@@ -2,21 +2,21 @@
 	<description>
 		BAM Parallelism Test
 	</description>
-	<parallelism method="basic" split_inputs="interval" split_mode='to_size' split_size='1' merge_outputs="output"/>
+	<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;
 
-		samtools view input.bam \$(cat $interval) | head -n 5 > $output;
+		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="interval" label="Interval File"/>
+		<param type="data" format="txt" name="infile" label="Interval File"/>
 	</inputs>
 	<outputs>
-		<data format="txt" name="output"/>
+		<data format="txt" name="outfile"/>
 	</outputs>
 </tool>
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