view sortBed.xml @ 5:b78d20957e7f draft

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<tool id="bedtools_sortbed" name="Sort BED files" version="0.2.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <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

@REFERENCES@

    </help>
</tool>