view BedToBam.xml @ 11:e526617a6bb9 draft

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<tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="0.1.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools bedtobam
        $ubam
        $bed12
        -mapq $mapq
        -i '$input'
        &gt; '$output'

    </command>
    <inputs>
        <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
        <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.."/>
        <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
        <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>

    </inputs>
    <outputs>
        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
    </outputs>
    <help>

**What it does**

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.

@REFERENCES@
    </help>
</tool>