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1 <tool id="samtools_slice_bam" name="Slice BAM" version="0.0.1">
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2 <description>by provided regions</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.18">samtools</requirement>
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5 </requirements>
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6 <command interpreter="python">samtools_slice_bam.py
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7 "${input_bam}"
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8 "${input_bam.metadata.bam_index}"
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9 "${input_interval}"
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10 "${output_bam}"
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11 </command>
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12 <inputs>
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13 <param name="input_bam" type="data" format="bam" label="BAM file" />
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14 <param name="input_interval" type="data" format="bed" label="BED file" />
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15 </inputs>
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16 <outputs>
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17 <data format="bam" name="output_bam"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
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22 <param name="input_interval" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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23 <output name="output_bam" file="gatk/fake_phiX_reads_1.bam" ftype="bam" />
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24 </test>
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25 </tests>
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26 <help>
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27 **What it does**
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28
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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.
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30
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31 ------
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32
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33 **Citation**
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34
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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>`_
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36
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37 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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38
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39 </help>
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40 </tool>
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