annotate flankBed.xml @ 1:82aac94b06c3 draft

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<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>
<![CDATA[
        flankBed
        $pct
        $strand
        -g $genome
        -i $input

        #if $addition.addition_select == 'b':
            -b $addition.b
        #else:
            -l $addition.l
            -r $addition.r
        #end if
        > $output
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" 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 metadata_source="input" format_source="input" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="a.bed" ftype="bed" />
            <param name="genome" value="mm9_chr1.len"/>
            <param name="addition_select" value="b"/>
            <param name="b" value="5"/>
            <output name="output" file="flankBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="input" value="a.bed" ftype="bed" />
            <param name="genome" value="mm9_chr1.len"/>
            <param name="addition_select" value="lr"/>
            <param name="l" value="2"/>
            <param name="r" value="3"/>
            <output name="output" file="flankBed_result2.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**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>