Mercurial > repos > marcoalbuquerque > bam_parallelism_test

comparison bam_parallelism_test.xml @ 10:b90e70fb1ac5 draft

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author marcoalbuquerque
date Mon, 02 Mar 2015 20:32:01 -0500
parents 06f281bbdf5b
children 219c97989aa7
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9:06f281bbdf5b 10:b90e70fb1ac5
6 <command> 6 <command>
7 7
8 ln -s $normal input.bam; 8 ln -s $normal input.bam;
9 ln -s $normal.metadata.bam_index input.bam.bai; 9 ln -s $normal.metadata.bam_index input.bam.bai;
10 10
11 samtools view input.bam \$(cat $infile) | head -n 5 > $outfile; 11 touch $outfile;
12
13 cat $infile;
14
15 echo \$(cat $infile);
16
17 samtools view input.bam \$(cat $infile) | head -n 5 >> $outfile;
12 18
13 </command> 19 </command>
14 <inputs> 20 <inputs>
15 <param type="data" format="bam" name="normal" label="Normal Alignment BAM"/> 21 <param type="data" format="bam" name="normal" label="Normal Alignment BAM"/>
16 22