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

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author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
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12:81d5b81fb3c2 13:eb53be9a09f4
1 <tool id="WigCorrelate" name="Correlate" version="1.0.0"> 1 <tool id="WigCorrelate" name="Correlate" version="1.0.0">
2 <description>multiple (Big)Wig files</description> 2 <description>multiple (Big)Wig files</description>
3 <command interpreter="sh"> 3 <command interpreter="sh">
4 galaxyToolRunner.sh wigmath.WigCorrelate -w $window -t $type -o $output 4 galaxyToolRunner.sh wigmath.WigCorrelate -w $window -s $step -t $type -o $output
5 #for $input in $inputs 5 #for $input in $inputs
6 ${input.file} 6 ${input.file}
7 #end for 7 #end for
8 </command> 8 </command>
9 <inputs> 9 <inputs>
10 <repeat name="inputs" title="(Big)Wig file"> 10 <repeat name="inputs" title="(Big)Wig file">
11 <param name="file" type="data" format="bigwig,wig" /> 11 <param name="file" type="data" format="bigwig,wig" />
12 </repeat> 12 </repeat>
13 <param name="window" type="integer" value="100" label="Window size (bp)" /> 13 <param name="window" type="integer" value="100" label="Window size (bp)" />
14 <param name="step" type="integer" value="50" label="Sliding step size (bp)" />
14 <param name="type" type="select" label="Correlation metric"> 15 <param name="type" type="select" label="Correlation metric">
15 <option value="pearson">Pearson</option> 16 <option value="pearson">Pearson</option>
16 <option value="spearman">Spearman</option> 17 <option value="spearman">Spearman</option>
17 </param> 18 </param>
18 </inputs> 19 </inputs>
20 <data format="tabular" name="output" /> 21 <data format="tabular" name="output" />
21 </outputs> 22 </outputs>
22 23
23 <help> 24 <help>
24 25
25 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 non-overlapping windows with the specified size 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. 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.
26 27
27 .. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient 28 .. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient
28 29
29 .. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient 30 .. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
31
32 -----
33
34 **Syntax**
35
36 - **Inputs** are the genomic data to correlate
37 - **Window size** is the size of the window to bin data into
38 - **Sliding step size** is the shift step size of the sliding window used during binning
39 - **Correlation metric** is the type of correlation to calculate
30 40
31 ----- 41 -----
32 42
33 .. class:: warningmark 43 .. class:: warningmark
34 44