Mercurial > repos > marcoalbuquerque > bam_parallelism_test
comparison bam_parallelism_test.xml @ 1:213289565e12 draft
Uploaded
| author | marcoalbuquerque |
|---|---|
| date | Sat, 28 Feb 2015 19:35:41 -0500 |
| parents | ab54013c8203 |
| children | 6ec7c93b90a6 |
comparison
equal
deleted
inserted
replaced
| 0:ab54013c8203 | 1:213289565e12 |
|---|---|
| 3 BAM Parallelism Test | 3 BAM Parallelism Test |
| 4 </description> | 4 </description> |
| 5 <parallelism method="multi" split_inputs="normal,tumour" split_mode="by_rname" real_split="False" merge_outputs="output"/> | 5 <parallelism method="multi" split_inputs="normal,tumour" split_mode="by_rname" real_split="False" merge_outputs="output"/> |
| 6 <command> | 6 <command> |
| 7 | 7 |
| 8 { | 8 cat interval.txt; |
| 9 samtools view -H $normal; | |
| 10 samtools view $normal \$(echo interval.txt) | head -n5; | |
| 11 samtools view $tumour \$(echo interval.txt) | head -n5; | |
| 12 } | samtools view -bS - > $output; | |
| 13 | 9 |
| 14 </command> | 10 </command> |
| 15 <inputs> | 11 <inputs> |
| 16 <param type="data" format="bam" name="normal" label="Normal Alignment BAM"/> | 12 <param type="data" format="bam" name="normal" label="Normal Alignment BAM"/> |
| 17 <param type="data" format="bam" name="tumour" label="Tumour Alignment BAM"/> | 13 <param type="data" format="bam" name="tumour" label="Tumour Alignment BAM"/> |