Mercurial > repos > iuc > bedtools

comparison groupbyBed.xml @ 1:82aac94b06c3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 607c0576c6ab
comparison
equal deleted inserted replaced
0:b8348686a0b9 1:82aac94b06c3
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 bedtools groupby 10 bedtools groupby
10 -c $cols 11 -c "${cols}"
11 -g $group 12 -g $group
12 -o $operation 13 -o $operation
13 -i $inputA 14 -i "${inputA}"
14 &gt; $output 15 > "${output}"
16 ]]>
15 </command> 17 </command>
16 <inputs> 18 <inputs>
17 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 19 <param format="bed" name="inputA" type="data" label="BED file"/>
18 <param name="cols" type="text" value="" label="Specify the column(s) (comma separated) that should be summarized" /> 20 <expand macro="choose_columns" />
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." /> 21 <param name="group" type="text" value="1,2,3"
20 <param name="operation" type="select" label="Specify the operation"> 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)">
21 <option value="sum" selected="True">Sum - numeric only</option> 29 <option value="sum" selected="True">Sum - numeric only</option>
22 <option value="stdev">Stdev - numeric only</option> 30 <option value="stdev">Stdev - numeric only</option>
23 <option value="sstdev">Sstdev - numeric only</option> 31 <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> 32 <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</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> 33 <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
26 <option value="first">First - numeric or text</option> 34 <option value="first">First - numeric or text</option>
27 <option value="last">Last - numeric or text</option> 35 <option value="last">Last - numeric or text</option>
28 <expand macro="math_options" /> 36 <expand macro="math_options" />
29 <expand macro="additional_math_options" /> 37 <expand macro="additional_math_options" />
30 </param> 38 </param>
31 </inputs> 39 </inputs>
32 <outputs> 40 <outputs>
33 <data format_source="inputA" name="output" metadata_source="inputA" label=""/> 41 <data format_source="inputA" name="output" metadata_source="inputA"/>
34 </outputs> 42 </outputs>
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>
35 <help> 66 <help>
36 67 <![CDATA[
37 **What it does** 68 **What it does**
38 69
39 Replicate lines in a file based on columns of comma-separated values. 70 Replicate lines in a file based on columns of comma-separated values.
40 71
41 @REFERENCES@ 72 @REFERENCES@
73 ]]>
42 </help> 74 </help>
43 <expand macro="citations" /> 75 <expand macro="citations" />
44 </tool> 76 </tool>