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comparison randomBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 457b09031d57
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0:b8348686a0b9 1:82aac94b06c3
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 bedtools random 10 bedtools random
10 -g $genome 11 -g $genome
11 -l $length 12 -l $length
12 -n $intervals 13 -n $intervals
13 #if $seed.choose: 14 #if $seed.seed_choose:
14 -seed $seed.seed 15 -seed $seed.seed
15 #end if 16 #end if
17 > "$output"
18 ]]>
16 </command> 19 </command>
17 <inputs> 20 <inputs>
18 <expand macro="genome" /> 21 <expand macro="genome" />
19 <param name="length" type="integer" value="100" label="The length of the intervals to generate." /> 22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" />
20 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate." /> 23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
21 <expand macro="seed" /> 24 <expand macro="seed" />
22 </inputs> 25 </inputs>
23 <outputs> 26 <outputs>
24 <data format="bed" name="output" /> 27 <data format="bed" name="output" />
25 </outputs> 28 </outputs>
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>
26 <help> 39 <help>
27 40 <![CDATA[
28 **What it does** 41 **What it does**
29 42
30 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. 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.
31 44
32 @REFERENCES@ 45 @REFERENCES@
46 ]]>
33 </help> 47 </help>
34 <expand macro="citations" /> 48 <expand macro="citations" />
35 </tool> 49 </tool>