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author devteam
date Tue, 20 Aug 2013 12:37:32 -0400
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1 <tool id="samtools_slice_bam" name="Slice BAM" version="0.0.1">
2 <description>by provided regions</description>
3 <requirements>
4 <requirement type="package" version="0.1.18">samtools</requirement>
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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
36
37 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
38
39 </help>
40 </tool>