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comparison randomBed.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_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>
9 <![CDATA[
10 bedtools random
11 -g $genome
12 -l $length
13 -n $intervals
14 #if str($seed.seed_choose) == "True":
15 -seed $seed.seed
16 #end if
17 > "$output"
18 ]]>
19 </command>
20 <inputs>
21 <expand macro="genome" />
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)" />
24 <expand macro="seed" />
25 </inputs>
26 <outputs>
27 <data format="bed" name="output" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="genome" value="mm9_chr1.len" />
32 <param name="seed_choose" value="False" />
33 <param name="length" value="5" />
34 <param name="intervals" value="3" />
35 <output name="output">
36 <assert_contents>
37 <has_text_matching expression="chr1" />
38 <has_n_columns n="6" />
39 </assert_contents>
40 </output>
41 </test>
42 </tests>
43 <help>
44 <![CDATA[
45 **What it does**
46
47 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.
48
49 @REFERENCES@
50 ]]>
51 </help>
52 <expand macro="citations" />
53 </tool>