sortBed.xml

<tool id="bedtools_sortbed" name="Sort BED" version="2.18.2.0">
    <description>files</description>
    <requirements>
        <requirement type="package" version="2.18.2">bedtools2</requirement>
    </requirements>
    <version_command>bedtools --version</version_command>
    <command>
        sortBed -i $input $option &gt; $output
    </command>
        <inputs>
            <param format="bed" name="input" type="data" label="Sort the following BED file"/>
            <param name="option" type="select" label="Sort by">
            <!-- sort -k 1,1 -k2,2 -n a.bed -->
            <option value="">chromosome, then by start position (asc)</option>
            <option value="-sizeA">feature size in ascending order.</option>
            <option value="-sizeD">feature size in descending order.</option>
            <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
            <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
            <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
            <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
        </param>
    </inputs>

    <outputs>
        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
    </outputs>
    <help>

**What it does**

Sorts a feature file by chromosome and other criteria.


.. class:: warningmark

It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed

------

This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__

    .. __: http://code.google.com/p/bedtools/
    .. __: http://cphg.virginia.edu/quinlan/
    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short

    </help>
</tool>