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comparison galaxy-conf/PowerSpectrum.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 4b32ed5d4a1b
children
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11:b1952a90d4bf 12:81d5b81fb3c2
1 <tool id="PowerSpectrum" name="Compute the power spectrum" version="1.0.0"> 1 <tool id="PowerSpectrum" name="Compute the power spectrum" version="1.0.0">
2 <description>on data in a Wiggle file</description> 2 <description>of data in a Wiggle file</description>
3 <command interpreter="sh">galaxyToolRunner.sh ngs.PowerSpectrum -i $input -l $windows -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh ngs.PowerSpectrum -i $input -l $windows -m $max -o $output</command>
4 <inputs> 4 <inputs>
5 <param format="bigwig,wig" name="input" type="data" label="Input data" /> 5 <param format="bigwig,wig" name="input" type="data" label="Input data" />
6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" /> 6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
7 <param name="max" type="integer" value="40" label="Number of frequencies to output" />
7 </inputs> 8 </inputs>
8 <outputs> 9 <outputs>
9 <data format="tabular" name="output" /> 10 <data format="tabular" name="output" />
10 </outputs> 11 </outputs>
11 12
12 <help> 13 <help>
14
15 This tool computes the power spectrum of intervals of sequencing data. For each interval provided, the normalized power spectrum is calculated, representing the relative power in each frequency. Power spectra are normalized to have total power 1, with the DC component (0 frequency) removed. Power spectra are computed using the FFT_ implementation in JTransforms_.
16
17 .. _FFT: http://en.wikipedia.org/wiki/Fast_Fourier_transform
18
19 .. _JTransforms: http://sites.google.com/site/piotrwendykier/software/jtransforms
20
21 -----
22
23 **Syntax**
24
25 - **Input data** is the genomic data on which to compute the power spectrum.
26 - **List of intervals:** The power spectrum will be computed for each genomic interval specified in this list.
27 - **Number of frequencies:** The power spectrum will be truncated at this frequency in the output
28
29 -----
30
31 **Output**
32
33 The output has the following format ::
34
35 chr start stop id alignment strand freq1 freq2 ...
36
37 up to the maximum frequency specified. Frequencies are truncated to reduce the size of the output since signals are often band-limited.
38
39 -----
40
13 .. class:: warningmark 41 .. class:: warningmark
14 42
15 This tool requires Wiggle/BigWig input data. 43 **NOTE:** Even though frequencies may be truncated in the output, all frequencies in the power spectrum are computed and used for normalization.
44
45 .. class:: infomark
46
47 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly. Intervals must be provided in Bed, BedGraph, or GFF format.
48
49 -----
50
51 This tool is equivalent to the following Matlab commands, where x is a vector with the interval of sequencing data ::
52
53 N = length(x);
54 f = fft(x);
55 p = abs(f(2:N/2)).^2;
56 p = p / sum(p);
57
16 </help> 58 </help>
17 </tool> 59 </tool>