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1 <tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0">
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6
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 bedtools groupby
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10 -c $cols
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11 -g $group
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12 -o $operation
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13 -i $inputA
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14 > $output
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15 </command>
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16 <inputs>
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17 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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18 <param name="cols" type="text" value="" label="Specify the column(s) (comma separated) that should be summarized" />
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19 <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." />
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20 <param name="operation" type="select" label="Specify the operation">
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21 <option value="sum" selected="True">Sum - numeric only</option>
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22 <option value="stdev">Stdev - numeric only</option>
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23 <option value="sstdev">Sstdev - numeric only</option>
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24 <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>
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25 <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>
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26 <option value="first">First - numeric or text</option>
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27 <option value="last">Last - numeric or text</option>
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28 <expand macro="math_options" />
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29 <expand macro="additional_math_options" />
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
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34 </outputs>
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35 <help>
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36
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37 **What it does**
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38
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39 Replicate lines in a file based on columns of comma-separated values.
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40
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41 @REFERENCES@
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42 </help>
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43 </tool>
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