|
0
|
1 <tool id="bedtools_randombed" name="RandomBed" 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>
|
|
4
|
9 <![CDATA[
|
|
0
|
10 bedtools random
|
|
|
11 -g $genome
|
|
|
12 -l $length
|
|
|
13 -n $intervals
|
|
4
|
14 #if $seed.seed_choose:
|
|
|
15 -seed $seed.seed
|
|
0
|
16 #end if
|
|
4
|
17 > "$output"
|
|
|
18 ]]>
|
|
0
|
19 </command>
|
|
|
20 <inputs>
|
|
|
21 <expand macro="genome" />
|
|
4
|
22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" />
|
|
|
23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
|
|
0
|
24 <expand macro="seed" />
|
|
|
25 </inputs>
|
|
|
26 <outputs>
|
|
|
27 <data format="bed" name="output" />
|
|
|
28 </outputs>
|
|
4
|
29 <tests>
|
|
|
30 <test>
|
|
|
31 <param name="genome" value="mm9_chr1.len" />
|
|
|
32 <param name="seed_choose" value="True" />
|
|
|
33 <param name="seed" value="1" />
|
|
|
34 <param name="length" value="5" />
|
|
|
35 <param name="intervals" value="3" />
|
|
|
36 <output name="output" file="randomBed_result1.bed" ftype="bed" />
|
|
|
37 </test>
|
|
|
38 </tests>
|
|
0
|
39 <help>
|
|
4
|
40 <![CDATA[
|
|
0
|
41 **What it does**
|
|
|
42
|
|
|
43 bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.
|
|
|
44
|
|
|
45 @REFERENCES@
|
|
4
|
46 ]]>
|
|
0
|
47 </help>
|
|
1
|
48 <expand macro="citations" />
|
|
0
|
49 </tool>
|
