view flankbed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        flankBed
        $pct
        $strand
        -g $genome
        -i $inputA

        #if $addition.addition_select == 'b':
            -b $addition.b
        #else:
            -l $addition.l
            -r $addition.r
        #end if

        &gt; $output
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <expand macro="genome" />
        <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
        <expand macro="addition" />
    </inputs>
    <outputs>
        <data format="bed" name="output"  label=""/>
    </outputs>
    <help>

**What it does**

bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.

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

.. class:: warningmark

In order to prevent creating intervals that violate chromosome boundaries, bedtools flank requires a genome file defining the length of each chromosome or contig.

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