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annotate galaxy-conf/PercusDecomposition.xml @ 12:81d5b81fb3c2 draft

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Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents b1952a90d4bf
children 3e477c7e0e73
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1 <tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.0.0">
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2 <description>from occupancy data</description>
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3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output</command>
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4 <inputs>
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5 <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts (smoothed)" />
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6 <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" />
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="wig" />
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10 </outputs>
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12 <help>
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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14 This tool derives an external potential energy function from experimental nucleosome positioning data by assuming that nucleosomes interact with DNA like a fluid of hard rods. This energy function can then be used to derive sequence-specific nucleosome formation preferences, while accounting for hard-core steric restriction by adjacent nucleosomes. This tool is a reimplementation of the algorithm described in (Locke et al. 2010).
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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16 -----
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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18 **Citations**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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20 Locke G, Tolkunov D, Moqtaderi Z, Struhl K and Morozov AV (2010) High-throughput sequencing reveals a simple model of nucleosome energetics. Proceedings of the National Academy of Sciences 107: 20998–21003
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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22 Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511
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24 </help>
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25 </tool>