Mercurial > repos > iuc > bedtools
comparison groupbyBed.xml @ 0:4fb5ea02b441 draft
Uploaded
| author | iuc |
|---|---|
| date | Tue, 15 Jul 2014 14:42:23 -0400 |
| parents | |
| children | 7511823bdea1 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:4fb5ea02b441 |
|---|---|
| 1 <tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 bedtools groupby | |
| 10 -c $cols | |
| 11 -g $group | |
| 12 -o $operation | |
| 13 -i $inputA | |
| 14 > $output | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 18 <param name="cols" type="text" value="" label="Specify the column(s) (comma separated) that should be summarized" /> | |
| 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." /> | |
| 20 <param name="operation" type="select" label="Specify the operation"> | |
| 21 <option value="sum" selected="True">Sum - numeric only</option> | |
| 22 <option value="stdev">Stdev - numeric only</option> | |
| 23 <option value="sstdev">Sstdev - numeric only</option> | |
| 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> | |
| 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> | |
| 26 <option value="first">First - numeric or text</option> | |
| 27 <option value="last">Last - numeric or text</option> | |
| 28 <expand macro="math_options" /> | |
| 29 <expand macro="additional_math_options" /> | |
| 30 </param> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format_source="inputA" name="output" metadata_source="inputA" label=""/> | |
| 34 </outputs> | |
| 35 <help> | |
| 36 | |
| 37 **What it does** | |
| 38 | |
| 39 Replicate lines in a file based on columns of comma-separated values. | |
| 40 | |
| 41 @REFERENCES@ | |
| 42 </help> | |
| 43 </tool> |