Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/WigCorrelate.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 | |
| children | eb53be9a09f4 |
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| 11:b1952a90d4bf | 12:81d5b81fb3c2 |
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| 1 <tool id="WigCorrelate" name="Correlate" version="1.0.0"> | |
| 2 <description>multiple (Big)Wig files</description> | |
| 3 <command interpreter="sh"> | |
| 4 galaxyToolRunner.sh wigmath.WigCorrelate -w $window -t $type -o $output | |
| 5 #for $input in $inputs | |
| 6 ${input.file} | |
| 7 #end for | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <repeat name="inputs" title="(Big)Wig file"> | |
| 11 <param name="file" type="data" format="bigwig,wig" /> | |
| 12 </repeat> | |
| 13 <param name="window" type="integer" value="100" label="Window size (bp)" /> | |
| 14 <param name="type" type="select" label="Correlation metric"> | |
| 15 <option value="pearson">Pearson</option> | |
| 16 <option value="spearman">Spearman</option> | |
| 17 </param> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data format="tabular" name="output" /> | |
| 21 </outputs> | |
| 22 | |
| 23 <help> | |
| 24 | |
| 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 | |
| 27 .. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient | |
| 28 | |
| 29 .. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient | |
| 30 | |
| 31 ----- | |
| 32 | |
| 33 .. class:: warningmark | |
| 34 | |
| 35 **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. | |
| 36 | |
| 37 ----- | |
| 38 | |
| 39 **Citation** | |
| 40 | |
| 41 This tool was inspired by ACT_ from the Gerstein lab. | |
| 42 | |
| 43 .. _ACT: http://act.gersteinlab.org | |
| 44 | |
| 45 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. | |
| 46 | |
| 47 </help> | |
| 48 </tool> |