Mercurial > repos > devteam > samtools_slice_bam
annotate samtools_slice_bam.xml @ 1:e0a8a7f4da76 draft
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
| author | devteam |
|---|---|
| date | Thu, 27 Mar 2014 14:07:10 -0400 |
| parents | 8f9af81f2cfe |
| children | ea6104c707da |
| rev | line source |
|---|---|
|
1
e0a8a7f4da76
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
devteam
parents:
0
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1 <tool id="samtools_slice_bam" name="Slice BAM" version="0.0.2"> |
| 0 | 2 <description>by provided regions</description> |
| 3 <requirements> | |
|
1
e0a8a7f4da76
Uploaded tool and dependency definitions that specify samtools version 0.1.19.
devteam
parents:
0
diff
changeset
|
4 <requirement type="package" version="0.1.19">samtools</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python">samtools_slice_bam.py | |
| 7 "${input_bam}" | |
| 8 "${input_bam.metadata.bam_index}" | |
| 9 "${input_interval}" | |
| 10 "${output_bam}" | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <param name="input_bam" type="data" format="bam" label="BAM file" /> | |
| 14 <param name="input_interval" type="data" format="bed" label="BED file" /> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="bam" name="output_bam"/> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /> | |
| 22 <param name="input_interval" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> | |
| 23 <output name="output_bam" file="gatk/fake_phiX_reads_1.bam" ftype="bam" /> | |
| 24 </test> | |
| 25 </tests> | |
| 26 <help> | |
| 27 **What it does** | |
| 28 | |
| 29 Accepts an input BAM file and an input BED file and creates an output BAM file containing only those alignments that overlap the provided BED intervals. | |
| 30 | |
| 31 ------ | |
| 32 | |
| 33 **Citation** | |
| 34 | |
| 35 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ | |
| 36 | |
| 37 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* | |
| 38 | |
| 39 </help> | |
| 40 </tool> |