|
0
|
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>
|
|
1
|
9 <![CDATA[
|
|
0
|
10 bedtools groupby
|
|
1
|
11 -c "${cols}"
|
|
0
|
12 -g $group
|
|
|
13 -o $operation
|
|
1
|
14 -i "${inputA}"
|
|
|
15 > "${output}"
|
|
|
16 ]]>
|
|
0
|
17 </command>
|
|
|
18 <inputs>
|
|
1
|
19 <param format="bed" name="inputA" type="data" label="BED file"/>
|
|
|
20 <expand macro="choose_columns" />
|
|
|
21 <param name="group" type="text" value="1,2,3"
|
|
|
22 label="Specifies which column(s) (1-based) should be used to group the input"
|
|
|
23 help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)">
|
|
|
24 <sanitizer invalid_char="">
|
|
|
25 <valid initial="string.digits"><add value=","/><add value="-"/></valid>
|
|
|
26 </sanitizer>
|
|
|
27 </param>
|
|
|
28 <param name="operation" type="select" label="Specify the operation" help="(-o)">
|
|
0
|
29 <option value="sum" selected="True">Sum - numeric only</option>
|
|
|
30 <option value="stdev">Stdev - numeric only</option>
|
|
|
31 <option value="sstdev">Sstdev - numeric only</option>
|
|
1
|
32 <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
|
|
|
33 <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
|
|
0
|
34 <option value="first">First - numeric or text</option>
|
|
|
35 <option value="last">Last - numeric or text</option>
|
|
|
36 <expand macro="math_options" />
|
|
|
37 <expand macro="additional_math_options" />
|
|
|
38 </param>
|
|
|
39 </inputs>
|
|
|
40 <outputs>
|
|
1
|
41 <data format_source="inputA" name="output" metadata_source="inputA"/>
|
|
0
|
42 </outputs>
|
|
1
|
43 <tests>
|
|
|
44 <test>
|
|
|
45 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
|
|
|
46 <param name="cols" value="9" />
|
|
|
47 <param name="group" value="1,2,3" />
|
|
|
48 <param name="operation" value="sum" />
|
|
|
49 <output name="output" file="groupbyBed_result1.bed" ftype="bed" />
|
|
|
50 </test>
|
|
|
51 <test>
|
|
|
52 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
|
|
|
53 <param name="cols" value="9" />
|
|
|
54 <param name="group" value="1,2,3" />
|
|
|
55 <param name="operation" value="min" />
|
|
|
56 <output name="output" file="groupbyBed_result2.bed" ftype="bed" />
|
|
|
57 </test>
|
|
|
58 <test>
|
|
|
59 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
|
|
|
60 <param name="cols" value="9" />
|
|
|
61 <param name="group" value="1-4" />
|
|
|
62 <param name="operation" value="median" />
|
|
|
63 <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
|
|
|
64 </test>
|
|
|
65 </tests>
|
|
0
|
66 <help>
|
|
1
|
67 <![CDATA[
|
|
0
|
68 **What it does**
|
|
|
69
|
|
|
70 Replicate lines in a file based on columns of comma-separated values.
|
|
|
71
|
|
|
72 @REFERENCES@
|
|
1
|
73 ]]>
|
|
0
|
74 </help>
|
|
|
75 <expand macro="citations" />
|
|
|
76 </tool>
|
