view overlapBed.xml @ 22:bd7721ad15aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c

<tool id="bedtools_overlapbed" name="OverlapBed" version="@WRAPPER_VERSION@.0">
    <description>computes the amount of overlap from two intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools overlap
        -i '$input'
        -cols $cols
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
        <param name="cols" type="data_column" multiple="True" data_ref="input"
            label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance"
            help="The columns must be listed in the following order: start1,end1,start2,end2" />
    </inputs>
    <outputs>
        <data format_source="input" name="output" metadata_source="input" label="Overlap of ${input.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="windowBed_result1.bed" ftype="bed" />
            <param name="cols" value="2,3,5,6" />
            <output name="output" file="overlapBed_result1.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools.

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