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comparison spatial_proximity.xml @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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10:1558594a3c2e 11:b7f1d9f8f3bc
1 <tool id="spatialproximity" name="spatial proximity">
2 <description>of two interval sets</description>
3 <command interpreter="python">spatial_proximity.py $inputa $inputb $genome $outplot $outlog $outbed $strandness
4 </command>
5 <inputs>
6 <param name="inputa" format="interval" type="data" label="Interval set 1" />
7 <param name="inputb" format="interval" type="data" label="Interval set 2" />
8 <param name="genome" type="select" label="Select genome">
9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
11 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
12 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
13 </param>
14 <param name="strandness" type="select" label="Strand requirement" >
15 <option value="" selected="true"> none </option>
16 <option value="-s" > -s: closest feature on the same strand</option>
17 <option value="-S" > -S: closest feature on the opposite strand </option>
18 </param>
19 </inputs>
20 <outputs>
21 <data format="input" name="outbed" label="${tool.name} on ${on_string}: (bed)" />
22 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}: (plot)" />
23 <data format="txt" name="outlog" label="${tool.name} on ${on_string}: (log)" />
24 </outputs>
25 <help>
26
27 .. class:: infomark
28
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.
30
31 </help>
32 </tool>