<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>
<![CDATA[
        bedtools groupby
        -c "${cols}"
        -g $group
        -o $operation
        -i "${inputA}"
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bed" name="inputA" type="data" label="BED file"/>
        <expand macro="choose_columns" />
        <param name="group" type="text" value="1,2,3" 
            label="Specifies which column(s) (1-based) should be used to group the input"
            help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)">
            <sanitizer invalid_char="">
                <valid initial="string.digits"><add value=","/><add value="-"/></valid>
            </sanitizer>
        </param>
        <param name="operation" type="select" label="Specify the operation" help="(-o)">
            <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 - comma separated list of values observed and the number of times they were observed (ascending)</option>
            <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</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"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
            <param name="cols" value="9" />
            <param name="group" value="1,2,3" />
            <param name="operation" value="sum" />
            <output name="output" file="groupbyBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
            <param name="cols" value="9" />
            <param name="group" value="1,2,3" />
            <param name="operation" value="min" />
            <output name="output" file="groupbyBed_result2.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
            <param name="cols" value="9" />
            <param name="group" value="1-4" />
            <param name="operation" value="median" />
            <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

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

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