<tool id="samtools_slice_bam" name="Slice BAM" version="0.0.1">
  <description>by provided regions</description>
  <requirements>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">samtools_slice_bam.py
    "${input_bam}"
    "${input_bam.metadata.bam_index}"
    "${input_interval}"
    "${output_bam}"
  </command>
  <inputs>
    <param name="input_bam" type="data" format="bam" label="BAM file" />
    <param name="input_interval" type="data" format="bed" label="BED file" />
  </inputs>
  <outputs>
    <data format="bam" name="output_bam"/>
  </outputs>
  <tests>
      <test>
          <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
          <param name="input_interval" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
          <output name="output_bam" file="gatk/fake_phiX_reads_1.bam" ftype="bam" />
      </test>
  </tests>
  <help>
**What it does**

 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.

------

**Citation**

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;`_

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

  </help>
</tool>