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1 <tool id="FindNuke" name="Find boundary nucleosomes" version="1.0.0">
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2 <description>in windows</description>
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3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="nukes" label="Nucleosome calls" />
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6 <param name="loci" type="data" format="bed" label="List of intervals" />
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="bed" metadata_source="loci" />
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10 </outputs>
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11
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12 <help>
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13 .. class:: warningmark
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14
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15 Use the Greedy Caller tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position from the 5' or 3' end.
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16 </help>
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17 </tool>
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