annotate galaxy-conf/KMeans.xml @ 15:3e477c7e0e73 draft

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 81d5b81fb3c2
children
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1 <tool id="KMeans" name="KMeans cluster" version="1.0.0">
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2 <description>an aligned matrix</description>
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3 <command interpreter="sh">galaxyToolRunner.sh visualization.KMeans -i $input -k $K -1 $min -2 $max -o $output</command>
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4 <inputs>
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5 <param format="tabular" name="input" type="data" label="Aligned matrix" />
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6 <param name="K" type="integer" value="10" label="Number of clusters" />
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7 <param name="min" type="integer" value="1" label="Minimum column to use for clustering" />
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8 <param name="max" type="integer" value="-1" label="Maximum column to use for clustering (-1 to end)" />
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9 </inputs>
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10 <outputs>
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11 <data format="tabular" name="output" metadata="input" />
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12 </outputs>
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13 <tests>
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14 </tests>
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16 <help>
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18 .. class:: warningmark
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20 This tool requires tabular data in matrix2png format (with column AND row headers). For more information about the required format and usage instructions, see the matrix2png_ website.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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22 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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24 .. class:: infomark
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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26 You can use the "Align values in a matrix" tool to create a matrix, then use this tool to cluster the matrix with k-means.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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28 .. class:: infomark
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30 **TIP:** You can use the **min** and **max** columns to cluster a large matrix based on a subset of the columns. For example, you could cluster a 4000x4000 matrix on columns 200-300 by setting min = 200 and max = 300. This will greatly increase the efficiency of distance calculations during the k-means EM, and also allows you to cluster based on specific regions, such as promoters or coding sequences.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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32 -----
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34 This tool will cluster the rows in an aligned matrix with KMeans_. The implementation builds upon the KMeansPlusPlusClusterer available in commons-math3_.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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36 .. _KMeans: http://en.wikipedia.org/wiki/K-means_clustering
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38 .. _commons-math3: http://commons.apache.org/math/
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40 </help>
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41 </tool>