Mercurial > repos > cafletezbrant > kmersvm
view kmersvm/split_genome.xml @ 7:fd740d515502 draft default tip
Uploaded revised kmer-SVM to include modules from kmer-visual.
author | cafletezbrant |
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date | Sun, 16 Jun 2013 18:06:14 -0400 |
parents | 7fe1103032f7 |
children |
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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>