Mercurial > repos > timpalpant > java_genomics_toolkit
diff galaxy-conf/WaveletTransform.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 |
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children | b43c420a6135 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/WaveletTransform.xml Fri Jun 15 15:10:26 2012 -0400 @@ -0,0 +1,40 @@ +<tool id="WaveletTransform" name="Wavelet analysis" version="1.0.0"> + <description>across a genomic interval</description> + <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> + <inputs> + <param format="wig,bigwig" name="input" type="data" label="Sequencing data" /> + <param format="tabular" name="wavelet" type="data" label="Wavelet" /> + <param name="chr" type="text" label="Chromosome" /> + <param name="start" type="integer" value="1" label="Start base pair" /> + <param name="stop" type="integer" value="1000" label="Stop base pair" /> + <param name="min" type="integer" value="10" label="Minimum wavelet size (bp)" /> + <param name="max" type="integer" value="400" label="Maximum wavelet size (bp)" /> + <param name="N" type="integer" value="1" label="Scaling step size (bp)" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + +<help> + +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. + +.. _Wavelet: http://en.wikipedia.org/wiki/Wavelet + +.. _scaling: http://en.wikipedia.org/wiki/Scaleogram + +----- + +**Syntax** + +- **Input data** is the genomic data on which to compute the Wavelet scaling analysis. +- **Wavelet** a single column of values representing a discrete Wavelet. +- **Chromosome** a locus in the genome +- **Start base pair** a locus in the genome +- **Stop base pair** a locus in the genome +- **Minimum wavelet size** the smallest Wavelet to analyze +- **Minimum wavelet size** the largest Wavelet to analyze +- **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. + +</help> +</tool>