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comparison kmersvm/split_genome.xml @ 0:7fe1103032f7 draft

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author cafletezbrant
date Mon, 20 Aug 2012 18:07:22 -0400
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1 <tool id="kmersvm_genome_split" name="Split Genome">
2 <description>split genome into overlapping segments for feature prediction</description>
3 <command interpreter="python">scripts/split_genome.py -i $incr -s $size $bed_file</command>
4 <inputs>
5 <param name="size" type="integer" value="1000" label="Size of Fragmanent" />
6 <param name="incr" type="integer" value="500" label="Size of Overlap" />
7 <param format="tabular" name="bed_file" type="data" label="BED File of Regions for Prediction"/>
8 </inputs>
9 <outputs>
10 <data format="interval" name="split_genome_output.bed" from_work_dir="split_genome_output.bed" />
11 </outputs>
12 <tests>
13 <test>
14 <param name="size" value="100" />
15 <param name="incr" value="20" />
16 <param name="bed_file" value="nullseq_test.bed" ftype="tabular"/>
17 <output name="output" file="split_genome_output.bed" />
18 </test>
19 </tests>
20 <help>
21
22 **What it does**
23
24 Divides input genomic regions into regions of size N bp which overlap each other by N/2 bp. If genome-wide prediction is desired, a single BED file listing the total length of each chromosome should be provided as input.x
25
26 **Parameters**
27
28 Size of Genome Fragments: Size of regions into which genome will be split.
29
30 Size of Overlap: Size of overlap between genomic regions.
31
32 BED File of Regions for Prediction: Regions to be split according to above criteria.
33
34 ----
35
36 **Example**
37
38 Given a BED file, tool will output BED file of regions of length N, which overlap by N/2 bp::
39
40 chr1 0 1000
41 chr1 500 1500
42 chr1 1000 2000
43 chr1 1500 2500
44
45
46 </help>
47 </tool>