Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/DynaPro.xml @ 20:9d56b5b85740 draft
Reuploaded to see if tools get loaded correctly this time.
author | timpalpant |
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date | Fri, 15 Jun 2012 15:10:26 -0400 |
parents | |
children | b43c420a6135 |
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1 <tool id="DynaPro" name="Compute equilibrium nucleosome positions" version="1.1.0"> | |
2 <description>using DynaPro</description> | |
3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.DynaPro -i $input -n $N | |
4 #if str( $mean ) != '' | |
5 -m $mean | |
6 #end if | |
7 | |
8 #if str( $variance ) != '' | |
9 -v $variance | |
10 #end if | |
11 -o $output | |
12 </command> | |
13 <inputs> | |
14 <param format="bigwig,wig" name="input" type="data" label="Energy landscape" /> | |
15 <param name="N" type="integer" value="147" label="Nucleosome size (bp)" /> | |
16 <param name="mean" type="float" optional="true" label="Shift energy landscape to have mean" /> | |
17 <param name="variance" type="float" optional="true" label="Rescale energy landscape to have variance" /> | |
18 </inputs> | |
19 <outputs> | |
20 <data format="wig" name="output" metadata_source="input" /> | |
21 </outputs> | |
22 <help> | |
23 | |
24 .. class:: warningmark | |
25 | |
26 At present, this tool is only suitable for small genomes (yeast) since entire chromosomes must be loaded into memory. | |
27 | |
28 ----- | |
29 | |
30 Equilibrium nucleosome distribution is modeled as a one-dimensional fluid of hard rods adsorbing and moving within an external potential. This tool provides a simplified version of the DynaPro_ algorithm for a single factor interacting with hard-core repulsion. | |
31 | |
32 .. _DynaPro: http://nucleosome.rutgers.edu/nucleosome/ | |
33 | |
34 ----- | |
35 | |
36 **Syntax** | |
37 | |
38 - **Energy landscape** is the external potential function for each genomic base pair, and must be in Wig format. | |
39 - **Nucleosome size** is the hard-core interaction size. | |
40 | |
41 ----- | |
42 | |
43 **Citation** | |
44 | |
45 Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J and Siggia ED (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 37: 4707–4722. | |
46 | |
47 </help> | |
48 </tool> |