Mercurial > repos > marcoalbuquerque > bam_parallelism_test
comparison bam_parallelism_test.xml @ 4:0ec6a49b43df draft
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| author | marcoalbuquerque |
|---|---|
| date | Mon, 02 Mar 2015 20:03:55 -0500 |
| parents | a26d456c51dd |
| children | 44005870d0f3 |
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| 3:a26d456c51dd | 4:0ec6a49b43df |
|---|---|
| 3 BAM Parallelism Test | 3 BAM Parallelism Test |
| 4 </description> | 4 </description> |
| 5 <parallelism method="multi" split_inputs="interval" split_mode="by_rname" real_split="False" merge_outputs="output"/> | 5 <parallelism method="multi" split_inputs="interval" split_mode="by_rname" real_split="False" merge_outputs="output"/> |
| 6 <command> | 6 <command> |
| 7 | 7 |
| 8 samtools view $normal \$(cat $interval) | head -n 5 > $output; | 8 ln -s $normal input.bam |
| 9 samtools view $tumour \$(cat $interval) | head -n 5 >> $output; | 9 ln -s $normal.metadata.bam_index input.bam.bai |
| 10 | |
| 11 samtools view input.bam \$(cat $interval) | head -n 5 > $output; | |
| 10 | 12 |
| 11 </command> | 13 </command> |
| 12 <inputs> | 14 <inputs> |
| 13 <param type="data" format="bam" name="normal" label="Normal Alignment BAM"/> | 15 <param type="data" format="bam" name="normal" label="Normal Alignment BAM"/> |
| 14 <param type="data" format="bam" name="tumour" label="Tumour Alignment BAM"/> | 16 |
| 15 <param type="data" format="txt" name="interval" label="Interval File"/> | 17 <param type="data" format="txt" name="interval" label="Interval File"/> |
| 16 </inputs> | 18 </inputs> |
| 17 <outputs> | 19 <outputs> |
| 18 <data format="txt" name="output"/> | 20 <data format="txt" name="output"/> |
| 19 </outputs> | 21 </outputs> |