Mercurial > repos > marcoalbuquerque > bam_parallelism_test

changeset 13:8e718c9905e1 draft

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Uploaded
author marcoalbuquerque
date Tue, 03 Mar 2015 13:36:50 -0500
parents 37ede95b7061
children 5f30cdf6dbcc
files bam_parallelism_test.xml
diffstat 1 files changed, 3 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/bam_parallelism_test.xml	Mon Mar 02 20:36:01 2015 -0500
+++ b/bam_parallelism_test.xml	Tue Mar 03 13:36:50 2015 -0500
@@ -1,27 +1,15 @@
-<tool id="bam_parallelism_test" name="BAM Parallelism Test" version="2.4.1">
+<tool id="bam_parallelism_test" name="BAM Parallelism Test" version="1.0.0">
 	<description>
 		BAM Parallelism Test
 	</description>
-	<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1" shared_inputs="" merge_outputs="outfile"></parallelism>
+	<parallelism method="basic" 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;
-
-		echo "HELLO";
-
-		cat $infile;
-
-		echo \$(cat $infile);
-
-		samtools view input.bam \$(cat $infile) | head -n 5 >> $outfile;
-
+		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>