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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:34:27 -0400
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6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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1 <tool id="dwt_var1" name="Wavelet variance" version="1.0.2">
2
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2 <description>using Discrete Wavelet Transfoms</description>
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3 <requirements>
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4 <requirement type="package" version="1.0_6">r-bitops</requirement>
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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5 <requirement type="package" version="1.7.5">r-waveslim</requirement>
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6 <requirement type="package" version="4.6.8">r-wavethresh</requirement>
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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7 </requirements>
3
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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8 <command detect_errors="exit_code">
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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9 Rscript --vanilla '$__tool_directory__/execute_dwt_var_perFeature.R'
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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10 '$inputFile'
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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11 '$feature'
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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12 '$alpha'
2
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13 '$outputFile1'
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14 '$outputFile2'
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15 </command>
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16 <inputs>
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17 <param format="tabular" name="inputFile" type="data" label="Select data"/>
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18 <param name="feature" label="Feature column" type="data_column" data_ref="inputFile" multiple="true"
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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19 help="Please select at least one column"/>
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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20 <param name="alpha" type="float" value="0.05" label="alpha (significance level)" />
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21 </inputs>
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22 <outputs>
3
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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23 <data format="tabular" name="outputFile1" label="${tool.name} on ${on_string}: statistics"/>
6c29c7e347e8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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24 <data format="pdf" name="outputFile2" label="${tool.name} on ${on_string}: pdf"/>
2
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="inputFile" value="dwt_var_in.interval"/>
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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29 <param name="feature" value="4"/>
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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30 <param name="alpha" value="0.05"/>
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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31 <output name="outputFile1" file="dwt_var_out1.tabular" compare="re_match"/>
7a15159140d1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature commit a684fffd461eea5ec33fe806fd2b6052c4321dcc
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32 <output name="outputFile2" file="dwt_var_out2.pdf" compare="sim_size"/>
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33 </test>
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34 </tests>
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35 <help>
0
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36
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37 .. class:: infomark
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38
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39 **What it does**
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40
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41 This tool computes the scale-specific variance in wavelet coeffients obtained from the discrete wavelet transform of a feature of interest.
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42
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43 Input data consists of an ordered series of data, S, equispaced and of sample size N, where N is of the form N = 2^k, and k is a positive integer and represents the number of levels of wavelet decomposition. S could be a time series, or a set of DNA sequences. The user calculates a statistic of interest for each feature in each interval of S: say, expression level of a particular gene in a time course, or the number of LINE elements per window across a chromosome. This tool then performs a discrete wavelet transform of the feature of interest, and plots the resulting variance in wavelet coefficients per wavelet scale. In addition, statistical significance of variances are determined by 1,000 random permutations of the intervals in S, to generate null bands (representing the user provided alpha value) corresponding to the empirical distribution of wavelet variances under the null hypothesis of no inherent order to the series in S.
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44
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45 This tool generates two output files:
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46
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47 - The first output file is a TABULAR format file representing the variances, p-values, and test orientation for the features at each wavelet scale based on a random permutation test.
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48 - The second output file is a PDF image plotting the wavelet variances of each feature at each scale.
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49
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50 -----
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51
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52 .. class:: warningmark
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53
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54 **Note**
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55 In order to obtain empirical p-values, a random perumtation scheme is implemented by the tool, such that the output may generate slightly variations in results each time it is run on the same input file.
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56
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57 </help>
0
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58 </tool>