Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/PercusDecomposition.xml @ 24:a77e126ae856 draft
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| author | timpalpant |
|---|---|
| date | Tue, 19 Jun 2012 22:15:09 -0400 |
| parents | 9d56b5b85740 |
| children | b43c420a6135 |
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| 23:01d5d20eaadd | 24:a77e126ae856 |
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| 1 <tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.1.0"> | |
| 2 <description>from occupancy data</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output</command> | |
| 4 <inputs> | |
| 5 <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts (smoothed)" /> | |
| 6 <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" /> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data name="output" format="wig" /> | |
| 10 </outputs> | |
| 11 | |
| 12 <help> | |
| 13 | |
| 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). | |
| 15 | |
| 16 ----- | |
| 17 | |
| 18 **Citations** | |
| 19 | |
| 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 | |
| 21 | |
| 22 Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511 | |
| 23 | |
| 24 </help> | |
| 25 </tool> |