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1 <tool id="spatialproximity" name="spatial proximity">
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2 <description>of two interval sets</description>
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3 <command interpreter="python">spatial_proximity.py $inputa $inputb $genome $outplot $outlog $outbed $strandness
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4 </command>
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5 <inputs>
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6 <param name="inputa" format="interval" type="data" label="Interval set 1" />
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7 <param name="inputb" format="interval" type="data" label="Interval set 2" />
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8 <param name="genome" type="select" label="Select genome">
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9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
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10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
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11 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
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12 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
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13 </param>
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14 <param name="strandness" type="select" label="Strand requirement" >
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15 <option value="" selected="true"> none </option>
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16 <option value="-s" > -s: closest feature on the same strand</option>
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17 <option value="-S" > -S: closest feature on the opposite strand </option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="input" name="outbed" label="${tool.name} on ${on_string}: (bed)" />
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22 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}: (plot)" />
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23 <data format="txt" name="outlog" label="${tool.name} on ${on_string}: (log)" />
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24 </outputs>
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25 <help>
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26
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27 .. class:: infomark
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28
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29 for each feature in the first interval set, find the closest in the second set, then compared the distance distribution to shuffled set 1.
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30
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31 </help>
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32 </tool>
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