view groupbyBed.xml @ 12:c782e0edc4f1 draft default tip

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<tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools groupby
        -c $cols
        -g $group
        -o $operation
        -i $inputA
        &gt; $output
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <param name="cols" type="text" value="" label="Specify the column(s) (comma separated) that should be summarized" />
        <param name="group" type="text" value="1,2,3" label="Specifies which column(s) (1-based) should be used to group the input. Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed." />
        <param name="operation" type="select" label="Specify the operation">
            <option value="sum" selected="True">Sum - numeric only</option>
            <option value="stdev">Stdev - numeric only</option>
            <option value="sstdev">Sstdev - numeric only</option>
            <option value="freqasc">Freqasc - print a comma separated list of values observed and the number of times they were observed. Reported in ascending order of frequency*</option>
            <option value="freqdesc">Freqdesc - - print a comma separated list of values observed and the number of times they were observed. Reported in descending order of frequency*</option>
            <option value="first">First - numeric or text</option>
            <option value="last">Last - numeric or text</option>
            <expand macro="math_options" />
            <expand macro="additional_math_options" />
        </param>
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
    </outputs>
    <help>

**What it does**

Replicate lines in a file based on columns of comma-separated values.

@REFERENCES@
    </help>
</tool>