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comparison galaxy-conf/WaveletTransform.xml @ 15:3e477c7e0e73 draft

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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 eb53be9a09f4
children
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14:f58706d4d421 15:3e477c7e0e73
7 <param name="chr" type="text" label="Chromosome" /> 7 <param name="chr" type="text" label="Chromosome" />
8 <param name="start" type="integer" value="1" label="Start base pair" /> 8 <param name="start" type="integer" value="1" label="Start base pair" />
9 <param name="stop" type="integer" value="1000" label="Stop base pair" /> 9 <param name="stop" type="integer" value="1000" label="Stop base pair" />
10 <param name="min" type="integer" value="10" label="Minimum wavelet size (bp)" /> 10 <param name="min" type="integer" value="10" label="Minimum wavelet size (bp)" />
11 <param name="max" type="integer" value="400" label="Maximum wavelet size (bp)" /> 11 <param name="max" type="integer" value="400" label="Maximum wavelet size (bp)" />
12 <param name="N" type="integer" value="1" label="Step size (bp)" /> 12 <param name="N" type="integer" value="1" label="Scaling step size (bp)" />
13 </inputs> 13 </inputs>
14 <outputs> 14 <outputs>
15 <data format="tabular" name="output" /> 15 <data format="tabular" name="output" />
16 </outputs> 16 </outputs>
17 17
18 <help> 18 <help>
19 19
20 This tool will perform a Wavelet_ scaling_ analysis on an interval of genomic data. For each base pair in the interval, the similarity (correlation) is calculated between the data and the wavelet over a range of scales. This can be used to identify high-frequency and low-frequency features in the data. The output is a matrix in matrix2png format that can be used to generate a heatmap: along the x-axis (columns) are the base pairs in the interval, along the y-axis (rows) are the correlation coefficients for each Wavelet size, with the largest Wavelet scale at the top and the smallest scale at the bottom.
21
22 .. _Wavelet: http://en.wikipedia.org/wiki/Wavelet
23
24 .. _scaling: http://en.wikipedia.org/wiki/Scaleogram
25
26 -----
27
28 **Syntax**
29
30 - **Input data** is the genomic data on which to compute the Wavelet scaling analysis.
31 - **Wavelet** a single column of values representing a discrete Wavelet.
32 - **Chromosome** a locus in the genome
33 - **Start base pair** a locus in the genome
34 - **Stop base pair** a locus in the genome
35 - **Minimum wavelet size** the smallest Wavelet to analyze
36 - **Minimum wavelet size** the largest Wavelet to analyze
37 - **Scaling step size** the step size for the range of wavelet scales. The provided wavelet will be scaled to each size in the set min:step:max by interpolating the provided wavelet.
38
20 </help> 39 </help>
21 </tool> 40 </tool>