Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/PowerSpectrum.xml @ 13:eb53be9a09f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
1 <tool id="PowerSpectrum" name="Compute the power spectrum" version="1.0.0">
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
2 <description>of data in a Wiggle file</description>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh ngs.PowerSpectrum -i $input -l $windows -m $max -o $output</command>
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
4 <inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
5 <param format="bigwig,wig" name="input" type="data" label="Input data" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
7 <param name="max" type="integer" value="40" label="Number of frequencies to output" />
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
8 </inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
9 <outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
10 <data format="tabular" name="output" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
11 </outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
12
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
13 <help>
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
14
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
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_.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
16
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
17 .. _FFT: http://en.wikipedia.org/wiki/Fast_Fourier_transform
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
18
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
19 .. _JTransforms: http://sites.google.com/site/piotrwendykier/software/jtransforms
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
20
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
21 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
22
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
23 **Syntax**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
24
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
25 - **Input data** is the genomic data on which to compute the power spectrum.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
26 - **List of intervals:** The power spectrum will be computed for each genomic interval specified in this list.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
27 - **Number of frequencies:** The power spectrum will be truncated at this frequency in the output
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
28
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
29 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
30
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
31 **Output**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
32
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
33 The output has the following format ::
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
34
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
35 chr start stop id alignment strand freq1 freq2 ...
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
36
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
37 up to the maximum frequency specified. Frequencies are truncated to reduce the size of the output since signals are often band-limited.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
38
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
39 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
40
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
41 .. class:: warningmark
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
42
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
43 **NOTE:** Even though frequencies may be truncated in the output, all frequencies in the power spectrum are computed and used for normalization.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
44
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
45 .. class:: infomark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
46
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
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.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
48
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
49 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
50
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
51 This tool is equivalent to the following Matlab commands, where x is a vector with the interval of sequencing data ::
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
52
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
53 N = length(x);
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
54 f = fft(x);
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
55 p = abs(f(2:N/2)).^2;
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
56 p = p / sum(p);
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 4
diff changeset
57
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
58 </help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
59 </tool>