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1 <tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 bedtools bedtobam
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10 $ubam
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11 $bed12
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12 -mapq $mapq
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13 -i '$input'
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14 > '$output'
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15 </command>
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16 <inputs>
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17 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
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18 <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/>
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19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
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20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
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21 </inputs>
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22 <outputs>
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23 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
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24 </outputs>
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25 <help>
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26
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27 **What it does**
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28
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29 bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.
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30
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31 @REFERENCES@
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32 </help>
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33 <expand macro="citations" />
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34 </tool>
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