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comparison sortBed.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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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 &gt; $output
10 </command>
11 <inputs>
12 <param format="bed" name="input" type="data" label="Sort the following BED file"/>
13 <param name="option" type="select" label="Sort by">
14 <!-- sort -k 1,1 -k2,2 -n a.bed -->
15 <option value="">chromosome, then by start position (asc)</option>
16 <option value="-sizeA">feature size in ascending order.</option>
17 <option value="-sizeD">feature size in descending order.</option>
18 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
19 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
20 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
21 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
22 </param>
23 </inputs>
24
25 <outputs>
26 <data format="bed" name="output" metadata_source="input" label="${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 </tool>