annotate mapBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools map
        -a $inputA
        -b $inputB
        $strand
        -o $operation
        -c $col
        -f $overlap
        $reciprocal
        $split
        $header
        #if $genome.genome_choose == "-g" :
            -g $genome.genome
        #end if 
        &gt; $output
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file A"/>
        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file B"/>
        <param name="col" type="integer" value="5" label="Specify the column from the B file to map onto intervals in A" />
        <expand macro="overlap" />
        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Require reciprocal overlap." help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval." />
        <expand macro="strand2" />
        <param name="operation" type="select" label="Specify the operation">
            <option value="sum">Sum - numeric only</option>
            <option value="absmin">AbsMin - numeric only</option>
            <option value="absmax">AbsMax - numeric only</option>
            <expand macro="math_options" />
            <expand macro="additional_math_options" />
        </param>
        <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
        <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the A file prior to results." />
        <conditional name="genome">
            <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="" />
            <when value="-g">
                <expand macro="genome" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}"/>
    </outputs>
    <help>

**What it does**

bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.

.. image:: $PATH_TO_IMAGES/map-glyph.png

.. class:: infomark

bedtools map requires each input file to be sorted by genome coordinate. For BED files, this can be done with sort -k1,1 -k2,2n. Other sorting criteria are allowed if a genome file (-g) is provides that specifies the expected chromosome order.

.. class:: infomark

The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference.

@REFERENCES@

    </help>
    <expand macro="citations" />
</tool>