Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/WaveletTransform.xml @ 24:a77e126ae856 draft
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| author | timpalpant |
|---|---|
| date | Tue, 19 Jun 2012 22:15:09 -0400 |
| parents | 9d56b5b85740 |
| children | b43c420a6135 |
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| 23:01d5d20eaadd | 24:a77e126ae856 |
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| 1 <tool id="WaveletTransform" name="Wavelet analysis" version="1.0.0"> | |
| 2 <description>across a genomic interval</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh ngs.WaveletTransform -i $input -w $wavelet --chr $chr --start $start --stop $stop --min $min --max $max --step $N -o $output</command> | |
| 4 <inputs> | |
| 5 <param format="wig,bigwig" name="input" type="data" label="Sequencing data" /> | |
| 6 <param format="tabular" name="wavelet" type="data" label="Wavelet" /> | |
| 7 <param name="chr" type="text" label="Chromosome" /> | |
| 8 <param name="start" type="integer" value="1" label="Start 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)" /> | |
| 11 <param name="max" type="integer" value="400" label="Maximum wavelet size (bp)" /> | |
| 12 <param name="N" type="integer" value="1" label="Scaling step size (bp)" /> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="tabular" name="output" /> | |
| 16 </outputs> | |
| 17 | |
| 18 <help> | |
| 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 | |
| 39 </help> | |
| 40 </tool> |