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comparison groupbyBed.xml @ 0:b8348686a0b9 draft

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Imported from capsule None
author iuc
date Tue, 04 Nov 2014 01:45:04 -0500
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children 82aac94b06c3
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-1:000000000000 0:b8348686a0b9
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 &gt; $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 <expand macro="citations" />
44 </tool>