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41 lines
1.5 KiB
XML
41 lines
1.5 KiB
XML
<tool id="samtools_slice_bam" name="Slice BAM" version="0.0.1">
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<description>by provided regions</description>
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<requirements>
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<requirement type="package">samtools</requirement>
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</requirements>
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<command interpreter="python">samtools_slice_bam.py
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"${input_bam}"
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"${input_bam.metadata.bam_index}"
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"${input_interval}"
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"${output_bam}"
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</command>
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<inputs>
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<param name="input_bam" type="data" format="bam" label="BAM file" />
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<param name="input_interval" type="data" format="bed" label="BED file" />
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</inputs>
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<outputs>
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<data format="bam" name="output_bam"/>
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</outputs>
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<tests>
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<test>
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<param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
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<param name="input_interval" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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<output name="output_bam" file="gatk/fake_phiX_reads_1.bam" ftype="bam" />
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</test>
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</tests>
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<help>
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**What it does**
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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.
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------
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**Citation**
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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>`_
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If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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</help>
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</tool>
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