Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/KMeans.xml @ 22:727fbba02ef7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks.
author timpalpant
date Tue, 19 Jun 2012 22:09:23 -0400
parents 9d56b5b85740
children b43c420a6135
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
1 <tool id="KMeans" name="KMeans cluster" version="1.0.0">
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
2 <description>an aligned matrix</description>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh visualization.KMeans -i $input -k $K -1 $min -2 $max -o $output</command>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
4 <inputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
5 <param format="tabular" name="input" type="data" label="Aligned matrix" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
6 <param name="K" type="integer" value="10" label="Number of clusters" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
7 <param name="min" type="integer" value="1" label="Minimum column to use for clustering" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
8 <param name="max" type="integer" value="-1" label="Maximum column to use for clustering (-1 to end)" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
9 </inputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
10 <outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
11 <data format="tabular" name="output" metadata="input" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
12 </outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
13 <tests>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
14 </tests>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
15
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
16 <help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
17
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
18 .. class:: warningmark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
19
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
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.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
21
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
22 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
23
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
24 .. class:: infomark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
25
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
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.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
27
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
28 .. class:: infomark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
29
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
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.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
31
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
32 -----
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
33
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
34 This tool will cluster the rows in an aligned matrix with KMeans_. The implementation builds upon the KMeansPlusPlusClusterer available in commons-math3_.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
35
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
36 .. _KMeans: http://en.wikipedia.org/wiki/K-means_clustering
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
37
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
38 .. _commons-math3: http://commons.apache.org/math/
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
39
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
40 </help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
41 </tool>