Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/WigCorrelate.xml @ 12:81d5b81fb3c2 draft

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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
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children eb53be9a09f4
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12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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1 <tool id="WigCorrelate" name="Correlate" version="1.0.0">
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2 <description>multiple (Big)Wig files</description>
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3 <command interpreter="sh">
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4 galaxyToolRunner.sh wigmath.WigCorrelate -w $window -t $type -o $output
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5 #for $input in $inputs
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6 ${input.file}
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7 #end for
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8 </command>
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9 <inputs>
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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.
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11 <param name="file" type="data" format="bigwig,wig" />
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12 </repeat>
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13 <param name="window" type="integer" value="100" label="Window size (bp)" />
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14 <param name="type" type="select" label="Correlation metric">
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15 <option value="pearson">Pearson</option>
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16 <option value="spearman">Spearman</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data format="tabular" name="output" />
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21 </outputs>
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22
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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23 <help>
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24
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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.
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26
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27 .. _Pearson: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient
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28
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29 .. _Spearman: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
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30
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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31 -----
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32
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33 .. class:: warningmark
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34
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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.
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36
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37 -----
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38
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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39 **Citation**
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40
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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41 This tool was inspired by ACT_ from the Gerstein lab.
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42
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43 .. _ACT: http://act.gersteinlab.org
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44
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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.
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46
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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47 </help>
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48 </tool>