Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/WigCorrelate.xml @ 13:eb53be9a09f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
1 <tool id="WigCorrelate" name="Correlate" version="1.0.0">
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
2 <description>multiple (Big)Wig files</description>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
3 <command interpreter="sh">
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
4 galaxyToolRunner.sh wigmath.WigCorrelate -w $window -s $step -t $type -o $output
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
5 #for $input in $inputs
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
6 ${input.file}
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
7 #end for
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
8 </command>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
9 <inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
10 <repeat name="inputs" title="(Big)Wig file">
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
11 <param name="file" type="data" format="bigwig,wig" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
12 </repeat>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
13 <param name="window" type="integer" value="100" label="Window size (bp)" />
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
14 <param name="step" type="integer" value="50" label="Sliding step size (bp)" />
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
15 <param name="type" type="select" label="Correlation metric">
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
16 <option value="pearson">Pearson</option>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
17 <option value="spearman">Spearman</option>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
18 </param>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
19 </inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
20 <outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
21 <data format="tabular" name="output" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
22 </outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
23
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
24 <help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
25
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
26 This tool will compute a correlation matrix between the supplied Wig or BigWig files. Each row/column in the matrix is added in the order that files are added above, starting from the top left. The Wig file is downsampled into sliding windows with the specified bin size and shift by computing the mean value in each window. These windows are then correlated using either Pearson_'s Product-Moment correlation coefficient or Spearman_'s rank correlation coefficient. If the window size is set to 1, the correlation is calculated between all base pairs in the genome.
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
27
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
28 .. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
29
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
30 .. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
31
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
32 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
33
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
34 **Syntax**
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
35
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
36 - **Inputs** are the genomic data to correlate
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
37 - **Window size** is the size of the window to bin data into
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
38 - **Sliding step size** is the shift step size of the sliding window used during binning
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
39 - **Correlation metric** is the type of correlation to calculate
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
40
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
41 -----
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
42
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
43 .. class:: warningmark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
44
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
45 **WARN:** In order to calculate the correlation coefficient, the data is loaded into entirely into memory. For large genomes, this may require a lot of RAM unless comparably larger window sizes are used.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
46
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
47 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
48
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
49 **Citation**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
50
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
51 This tool was inspired by ACT_ from the Gerstein lab.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
52
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
53 .. _ACT: http://act.gersteinlab.org
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
54
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
55 J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein. ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011) Bioinformatics 27(8): 1152-4.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
56
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
57 </help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
58 </tool>