view bedToBam.xml @ 0:a993f4a9aeaa draft default tip

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<!-- adapted from https://toolshed.g2.bx.psu.edu/view/iuc/bedtools/f8b7dc21b4ee
     Added the samtools sort and samtools requirement as bam files must be outpit sorted -->
<tool id="bedtools_bedtobam_sorted" name="BED to sorted BAM" version="@WRAPPER_VERSION@.0">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" >
        <requirement type="package" version="1.2">samtools</requirement>
    </expand>
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools bedtobam
        $bed12
        -mapq $mapq
        -g $genome
        -i '$input'
        > unsorted.bam  &&
        samtools sort -@ \${GALAXY_SLOTS:-1} -o '$output' -O bam -T dataset 'unsorted.bam'
]]>
    </command>
    <inputs>
        <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
        <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
            label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
            help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/>
        <expand macro="genome" />
        <param name="mapq" type="integer" value="255"
            label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/>
    </inputs>
    <outputs>
        <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="bedToBam1.bed" ftype="bed" />
            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
            <output name="output" file="sortedBedToBam_result.bam" lines_diff="4" ftype="bam" />
        </test>
    </tests>
    <help>
<![CDATA[
**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>
    <expand macro="citations" />
</tool>