Mercurial > repos > xuebing > sharplab_interval_analysis
view spatial_proximity.xml @ 20:16ba480adf96
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author | xuebing |
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date | Sat, 31 Mar 2012 08:31:22 -0400 |
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<tool id="spatialproximity" name="spatial proximity"> <description>of two interval sets</description> <command interpreter="python">spatial_proximity.py $inputa $inputb $genome $outplot $outlog $outbed $strandness </command> <inputs> <param name="inputa" format="interval" type="data" label="Interval set 1" /> <param name="inputb" format="interval" type="data" label="Interval set 2" /> <param name="genome" type="select" label="Select genome"> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option> <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option> </param> <param name="strandness" type="select" label="Strand requirement" > <option value="" selected="true"> none </option> <option value="-s" > -s: closest feature on the same strand</option> <option value="-S" > -S: closest feature on the opposite strand </option> </param> </inputs> <outputs> <data format="input" name="outbed" label="${tool.name} on ${on_string}: (bed)" /> <data format="pdf" name="outplot" label="${tool.name} on ${on_string}: (plot)" /> <data format="txt" name="outlog" label="${tool.name} on ${on_string}: (log)" /> </outputs> <help> .. class:: infomark for each feature in the first interval set, find the closest in the second set, then compared the distance distribution to shuffled set 1. </help> </tool>