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date Wed, 08 Aug 2012 19:20:14 -0400
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1 <tool id="kmersvm_genome_split" name="Split Genome">
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2 <description>split genome into overlapping segments for feature prediction</description>
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3 <command interpreter="python">scripts/split_genome.py -i $incr -s $size $bed_file</command>
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4 <inputs>
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5 <param name="size" type="integer" value="1000" label="Size of Fragmanent" />
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6 <param name="incr" type="integer" value="500" label="Size of Overlap" />
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7 <param format="tabular" name="bed_file" type="data" label="BED File of Regions for Prediction"/>
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8 </inputs>
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9 <outputs>
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10 <data format="interval" name="split_genome_output.bed" from_work_dir="split_genome_output.bed" />
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11 </outputs>
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12 <tests>
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13 <test>
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14 <param name="size" value="100" />
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15 <param name="incr" value="20" />
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16 <param name="bed_file" value="nullseq_test.bed" ftype="tabular"/>
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17 <output name="output" file="split_genome_output.bed" />
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18 </test>
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19 </tests>
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20 <help>
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21
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22 **What it does**
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23
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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
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25
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26 **Parameters**
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27
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28 Size of Genome Fragments: Size of regions into which genome will be split.
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30 Size of Overlap: Size of overlap between genomic regions.
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31
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32 BED File of Regions for Prediction: Regions to be split according to above criteria.
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33
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34 ----
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35
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36 **Example**
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37
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38 Given a BED file, tool will output BED file of regions of length N, which overlap by N/2 bp::
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39
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40 chr1 0 1000
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41 chr1 500 1500
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42 chr1 1000 2000
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43 chr1 1500 2500
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46 </help>
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47 </tool>