Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/PercusDecomposition.xml @ 15:3e477c7e0e73 draft
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
| author | timpalpant |
|---|---|
| date | Sat, 09 Jun 2012 16:03:59 -0400 |
| parents | 81d5b81fb3c2 |
| children |
| rev | line source |
|---|---|
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15
3e477c7e0e73
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
parents:
12
diff
changeset
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1 <tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.1.0"> |
| 11 | 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> | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
13 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
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.
timpalpant
parents:
11
diff
changeset
|
15 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
16 ----- |
| 11 | 17 |
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12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
18 **Citations** |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
19 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
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.
timpalpant
parents:
11
diff
changeset
|
21 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
22 Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
23 |
| 11 | 24 </help> |
| 25 </tool> |