Mercurial > repos > ulfschaefer > phe_samtools_mpileup
comparison phe_samtools_mpileup.xml @ 11:714a4c13d64c draft
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| author | ulfschaefer |
|---|---|
| date | Mon, 21 Dec 2015 10:17:56 -0500 |
| parents | 0af0acbd73f7 |
| children | f8ca00a4ea23 |
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| 10:f78ed0f61f52 | 11:714a4c13d64c |
|---|---|
| 2 <description>PHE SNP and indel caller</description> | 2 <description>PHE SNP and indel caller</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.1">samtools</requirement> | 4 <requirement type="package" version="1.1">samtools</requirement> |
| 5 <requirement type="package" version="1.3">bcftools</requirement> | 5 <requirement type="package" version="1.3">bcftools</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <stdio> | |
| 8 <!-- Assume anything other than zero is an error --> | |
| 9 <exit_code range="1:" /> | |
| 10 <exit_code range=":-1" /> | |
| 11 </stdio> | |
| 7 <command interpreter="bash"> | 12 <command interpreter="bash"> |
| 8 phe_samtools_mpileup.sh $input_bam $ref_file $outvcf | 13 phe_samtools_mpileup.sh $input_bam $ref_file $outvcf |
| 9 </command> | 14 </command> |
| 10 <inputs> | 15 <inputs> |
| 11 <param name="input_bam" type="data" format="bam" label="BAM file" /> | 16 <param name="input_bam" type="data" format="bam" label="BAM file" /> |