comparison kmersvm/split_genome.xml @ 0:66088269713e draft

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<tool id="kmersvm_genome_split" name="Split Genome">
  <description>split genome into overlapping segments for feature prediction</description>
  <command interpreter="python">scripts/split_genome.py -i $incr -s $size $bed_file</command>
  <inputs>
    <param name="size" type="integer" value="1000" label="Size of Fragmanent" />
    <param name="incr" type="integer" value="500" label="Size of Overlap" />
    <param format="tabular" name="bed_file" type="data" label="BED File of Regions for Prediction"/>
  </inputs>
  <outputs>
    <data format="interval" name="split_genome_output.bed" from_work_dir="split_genome_output.bed" />
  </outputs>
  <tests>
    <test>
      <param name="size" value="100" />
      <param name="incr" value="20" />
      <param name="bed_file" value="nullseq_test.bed" ftype="tabular"/>
      <output name="output" file="split_genome_output.bed" />
    </test>
  </tests>
  <help>
  
**What it does**
  
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

**Parameters**
  
Size of Genome Fragments: Size of regions into which genome will be split.
  
Size of Overlap: Size of overlap between genomic regions.

BED File of Regions for Prediction: Regions to be split according to above criteria.

----
  
**Example**
  
Given a BED file, tool will output BED file of regions of length N, which overlap by N/2 bp::
  
    chr1	0	1000
    chr1	500	1500
    chr1	1000	2000
    chr1	1500	2500


  </help>
</tool>