Mercurial > repos > iuc > bedtools
comparison sortBed.xml @ 0:b8348686a0b9 draft
Imported from capsule None
author | iuc |
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date | Tue, 04 Nov 2014 01:45:04 -0500 |
parents | |
children | 82aac94b06c3 |
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-1:000000000000 | 0:b8348686a0b9 |
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1 <tool id="bedtools_sortbed" name="Sort BED files" 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 sortBed -i $input $option > $output | |
10 </command> | |
11 <inputs> | |
12 <param format="bed" name="input" type="data" label="Sort the following BED file"/> | |
13 <param name="option" type="select" label="Sort by"> | |
14 <!-- sort -k 1,1 -k2,2 -n a.bed --> | |
15 <option value="">chromosome, then by start position (asc)</option> | |
16 <option value="-sizeA">feature size in ascending order.</option> | |
17 <option value="-sizeD">feature size in descending order.</option> | |
18 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option> | |
19 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option> | |
20 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> | |
21 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> | |
22 </param> | |
23 </inputs> | |
24 | |
25 <outputs> | |
26 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> | |
27 </outputs> | |
28 | |
29 <help> | |
30 | |
31 **What it does** | |
32 | |
33 Sorts a feature file by chromosome and other criteria. | |
34 | |
35 | |
36 .. class:: warningmark | |
37 | |
38 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility | |
39 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file | |
40 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed | |
41 | |
42 @REFERENCES@ | |
43 | |
44 </help> | |
45 <expand macro="citations" /> | |
46 </tool> |