Mercurial > repos > xuebing > sharplabtool
comparison tools/mytools/spatial_proximity.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 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> |