Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/KMeans.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="KMeans" name="KMeans cluster" version="1.0.0"> | |
| 2 <description>an aligned matrix</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh visualization.KMeans -i $input -k $K -1 $min -2 $max -o $output</command> | |
| 4 <inputs> | |
| 5 <param format="tabular" name="input" type="data" label="Aligned matrix" /> | |
| 6 <param name="K" type="integer" value="10" label="Number of clusters" /> | |
| 7 <param name="min" type="integer" value="1" label="Minimum column to use for clustering" /> | |
| 8 <param name="max" type="integer" value="-1" label="Maximum column to use for clustering (-1 to end)" /> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data format="tabular" name="output" metadata="input" /> | |
| 12 </outputs> | |
| 13 <tests> | |
| 14 </tests> | |
| 15 | |
| 16 <help> | |
| 17 | |
| 18 .. class:: warningmark | |
| 19 | |
| 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. | |
| 21 | |
| 22 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html | |
| 23 | |
| 24 .. class:: infomark | |
| 25 | |
| 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. | |
| 27 | |
| 28 .. class:: infomark | |
| 29 | |
| 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. | |
| 31 | |
| 32 ----- | |
| 33 | |
| 34 This tool will cluster the rows in an aligned matrix with KMeans_. The implementation builds upon the KMeansPlusPlusClusterer available in commons-math3_. | |
| 35 | |
| 36 .. _KMeans: http://en.wikipedia.org/wiki/K-means_clustering | |
| 37 | |
| 38 .. _commons-math3: http://commons.apache.org/math/ | |
| 39 | |
| 40 </help> | |
| 41 </tool> |