Mercurial > repos > cafletezbrant > kmersvm
diff kmersvm/split_genome.xml @ 0:7fe1103032f7 draft
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author | cafletezbrant |
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date | Mon, 20 Aug 2012 18:07:22 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmersvm/split_genome.xml Mon Aug 20 18:07:22 2012 -0400 @@ -0,0 +1,47 @@ +<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>