Mercurial > repos > timpalpant > java_genomics_toolkit

annotate 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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1 <tool id="WaveletTransform" name="Wavelet analysis" version="1.0.0">
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2 <description>across a genomic interval</description>
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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>
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4 <inputs>
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5 <param format="wig,bigwig" name="input" type="data" label="Sequencing data" />
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6 <param format="tabular" name="wavelet" type="data" label="Wavelet" />
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7 <param name="chr" type="text" label="Chromosome" />
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8 <param name="start" type="integer" value="1" label="Start base pair" />
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9 <param name="stop" type="integer" value="1000" label="Stop base pair" />
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10 <param name="min" type="integer" value="10" label="Minimum wavelet size (bp)" />
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11 <param name="max" type="integer" value="400" label="Maximum wavelet size (bp)" />
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3e477c7e0e73 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.
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12 <param name="N" type="integer" value="1" label="Scaling step size (bp)" />
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13 </inputs>
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14 <outputs>
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15 <data format="tabular" name="output" />
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16 </outputs>
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17
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18 <help>
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19
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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.
3e477c7e0e73 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.
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3e477c7e0e73 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.
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22 .. _Wavelet: http://en.wikipedia.org/wiki/Wavelet
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3e477c7e0e73 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.
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24 .. _scaling: http://en.wikipedia.org/wiki/Scaleogram
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26 -----
3e477c7e0e73 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.
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27
3e477c7e0e73 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.
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28 **Syntax**
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30 - **Input data** is the genomic data on which to compute the Wavelet scaling analysis.
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31 - **Wavelet** a single column of values representing a discrete Wavelet.
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32 - **Chromosome** a locus in the genome
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33 - **Start base pair** a locus in the genome
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34 - **Stop base pair** a locus in the genome
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35 - **Minimum wavelet size** the smallest Wavelet to analyze
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36 - **Minimum wavelet size** the largest Wavelet to analyze
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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.
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39 </help>
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40 </tool>