Mercurial > repos > timpalpant > java_genomics_toolkit
diff galaxy-conf/KMeans.xml @ 12:81d5b81fb3c2 draft
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author | timpalpant |
---|---|
date | Wed, 25 Apr 2012 16:53:48 -0400 |
parents | b1952a90d4bf |
children |
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--- a/galaxy-conf/KMeans.xml Mon Apr 09 11:50:23 2012 -0400 +++ b/galaxy-conf/KMeans.xml Wed Apr 25 16:53:48 2012 -0400 @@ -14,5 +14,28 @@ </tests> <help> + +.. class:: warningmark + +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. + +.. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html + +.. class:: infomark + +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. + +.. class:: infomark + +**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. + +----- + +This tool will cluster the rows in an aligned matrix with KMeans_. The implementation builds upon the KMeansPlusPlusClusterer available in commons-math3_. + +.. _KMeans: http://en.wikipedia.org/wiki/K-means_clustering + +.. _commons-math3: http://commons.apache.org/math/ + </help> </tool>