Mercurial > repos > timpalpant > java_genomics_toolkit
diff 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 |
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date | Wed, 25 Apr 2012 16:53:48 -0400 |
parents | |
children | eb53be9a09f4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/WigCorrelate.xml Wed Apr 25 16:53:48 2012 -0400 @@ -0,0 +1,48 @@ +<tool id="WigCorrelate" name="Correlate" version="1.0.0"> + <description>multiple (Big)Wig files</description> + <command interpreter="sh"> + galaxyToolRunner.sh wigmath.WigCorrelate -w $window -t $type -o $output + #for $input in $inputs + ${input.file} + #end for + </command> + <inputs> + <repeat name="inputs" title="(Big)Wig file"> + <param name="file" type="data" format="bigwig,wig" /> + </repeat> + <param name="window" type="integer" value="100" label="Window size (bp)" /> + <param name="type" type="select" label="Correlation metric"> + <option value="pearson">Pearson</option> + <option value="spearman">Spearman</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + +<help> + +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. + +.. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient + +.. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient + +----- + +.. class:: warningmark + +**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. + +----- + +**Citation** + +This tool was inspired by ACT_ from the Gerstein lab. + +.. _ACT: http://act.gersteinlab.org + +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. + +</help> +</tool>