Mercurial > repos > xuebing > sharplabtool
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mytools/spatial_proximity.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,32 @@ +<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>