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comparison sortBed.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 0d3aa592ce27
children a2d4c30ba2f9
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9:21f1d1c5467b 10:71af3ebbbb7a
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 <![CDATA[
10 sortBed
11 -i $input
12 $option
13 > $output
14 ]]>
15 </command>
16 <inputs>
17 <param format="bed" name="input" type="data" label="Sort the following BED file"/>
18 <param name="option" type="select" label="Sort by">
19 <!-- sort -k 1,1 -k2,2 -n a.bed -->
20 <option value="">chromosome, then by start position (asc)</option>
21 <option value="-sizeA">feature size in ascending order.</option>
22 <option value="-sizeD">feature size in descending order.</option>
23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="input" value="sortBed1.bed" ftype="bed" />
35 <param name="option" value="" />
36 <output name="output" file="sortBed_result1.bed" ftype="bed" />
37 </test>
38 </tests>
39 <help>
40 <![CDATA[
41 **What it does**
42
43 Sorts a feature file by chromosome and other criteria.
44
45
46 .. class:: warningmark
47
48 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
49 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
50 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
51
52 @REFERENCES@
53 ]]>
54 </help>
55 <expand macro="citations" />
56 </tool>