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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:34:10 -0400
parents cb422b6f49d2
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781e68074f84 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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1 <tool id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" name="Compute P-values and Max Variances for Feature Occurrences" version="1.0.1">
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2 <description>in one dataset using Discrete Wavelet Transfoms</description>
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3 <requirements>
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4 <requirement type="package" version="1.7.5">r-waveslim</requirement>
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5 <requirement type="package" version="4.6.8">r-wavethresh</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 Rscript --vanilla '$__tool_directory__/execute_dwt_var_perClass.R'
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9 '$inputFile'
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10 '$outputFile1'
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11 '$outputFile2'
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12 '$outputFile3'
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13 </command>
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14 <inputs>
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15 <param format="tabular" name="inputFile" type="data" label="Select the input file"/>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="outputFile1" label="${tool.name} on ${on_string}: scales"/>
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19 <data format="tabular" name="outputFile2" label="${tool.name} on ${on_string}: statistics"/>
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20 <data format="pdf" name="outputFile3" label="${tool.name} on ${on_string}: pdf"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param ftype="tabular" name="inputFile" value="in.tsv"/>
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25 <output name="outputFile1" ftype="tabular">
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26 <assert_contents><has_line_matching expression="^max_var\tscale.*"/></assert_contents>
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27 <assert_contents><has_line_matching expression="^translinTarget.*" /></assert_contents>
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28 </output>
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29 <output name="outputFile2" ftype="tabular">
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30 <assert_contents><has_line_matching expression="^motif\t1_var.*"/></assert_contents>
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31 <assert_contents><has_line_matching expression="^translinTarget.*" /></assert_contents>
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32 </output>
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33 <output name="outputFile3" ftype="pdf" file="out.pdf" compare="sim_size"/>
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34 </test>
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35 </tests>
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36 <help>
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37
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38 .. class:: infomark
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39
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40 **What it does**
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41
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42 This program generates plots and computes table matrix of maximum variances, p-values, and test orientations at multiple scales for the occurrences of a class of features in one dataset of DNA sequences using multiscale wavelet analysis technique.
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43
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44 The program assumes that the user has one set of DNA sequences, S, which consists of one or more sequences of equal length. Each sequence in S is divided into the same number of multiple intervals n such that n = 2^k, where k is a positive integer and k >= 1. Thus, n could be any value of the set {2, 4, 8, 16, 32, 64, 128, ...}. k represents the number of scales.
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45
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46 The program has one input file obtained as follows:
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47
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48 For a given set of features, say motifs, the user counts the number of occurrences of each feature in each interval of each sequence in S, and builds a tabular file representing the count results in each interval of S. This is the input file of the program.
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49
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50 The program gives three output files:
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51
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52 - The first output file is a TABULAR format file giving the scales at which each features has a maximum variances.
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53 - The second output file is a TABULAR format file representing the variances, p-values, and test orientation for the occurrences of features at each scale based on a random permutation test and using multiscale wavelet analysis technique.
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54 - The third output file is a PDF file plotting the wavelet variances of each feature at each scale.
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55
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56 -----
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57
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58 .. class:: warningmark
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59
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60 **Note**
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61
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62 - If the number of features is greater than 12, the program will divide each output file into subfiles, such that each subfile represents the results of a group of 12 features except the last subfile that will represents the results of the rest. For example, if the number of features is 17, the p-values file will consists of two subfiles, the first for the features 1-12 and the second for the features 13-17. As for the PDF file, it will consists of two pages in this case.
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63 - In order to obtain empirical p-values, a random perumtation test is implemented by the program, which results in the fact that the program gives slightly different results each time it is run on the same input file.
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64
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65 -----
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66
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67
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68 **Example**
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69
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70 Counting the occurrences of 8 features (motifs) in 16 intervals (one line per interval) of set of DNA sequences in S gives the following tabular file::
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71
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72 deletionHoptspot insertionHoptspot dnaPolPauseFrameshift indelHotspot topoisomeraseCleavageSite translinTarget vDjRecombinationSignal x-likeSite
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73 226 403 416 221 1165 832 749 1056
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74 236 444 380 241 1223 746 782 1207
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75 242 496 391 195 1116 643 770 1219
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76 243 429 364 191 1118 694 783 1223
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77 244 410 371 236 1063 692 805 1233
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78 230 386 370 217 1087 657 787 1215
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79 275 404 402 214 1044 697 831 1188
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80 265 443 365 231 1086 694 782 1184
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81 255 390 354 246 1114 642 773 1176
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82 281 384 406 232 1102 719 787 1191
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83 263 459 369 251 1135 643 810 1215
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84 280 433 400 251 1159 701 777 1151
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85 278 385 382 231 1147 697 707 1161
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86 248 393 389 211 1162 723 759 1183
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87 251 403 385 246 1114 752 776 1153
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88 239 383 347 227 1172 759 789 1141
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89
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90 We notice that the number of scales here is 4 because 16 = 2^4. Runnig the program on the above input file gives the following 3 output files:
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91
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92 The first output file::
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93
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94 motifs max_var at scale
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95 deletionHoptspot NA
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96 insertionHoptspot NA
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97 dnaPolPauseFrameshift NA
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98 indelHotspot NA
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99 topoisomeraseCleavageSite 3
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100 translinTarget NA
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101 vDjRecombinationSignal NA
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102 x.likeSite NA
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103
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104 The second output file::
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105
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106 motif 1_var 1_pval 1_test 2_var 2_pval 2_test 3_var 3_pval 3_test 4_var 4_pval 4_test
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107
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108 deletionHoptspot 0.457 0.048 L 1.18 0.334 R 1.61 0.194 R 3.41 0.055 R
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109 insertionHoptspot 0.556 0.109 L 1.34 0.272 R 1.59 0.223 R 2.02 0.157 R
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110 dnaPolPauseFrameshift 1.42 0.089 R 0.66 0.331 L 0.421 0.305 L 0.121 0.268 L
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111 indelHotspot 0.373 0.021 L 1.36 0.254 R 1.24 0.301 R 4.09 0.047 R
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112 topoisomeraseCleavageSite 0.305 0.002 L 0.936 0.489 R 3.78 0.01 R 1.25 0.272 R
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113 translinTarget 0.525 0.061 L 1.69 0.11 R 2.02 0.131 R 0.00891 0.069 L
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114 vDjRecombinationSignal 0.68 0.138 L 0.957 0.46 R 2.35 0.071 R 1.03 0.357 R
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115 x.likeSite 0.928 0.402 L 1.33 0.261 R 0.735 0.431 L 0.783 0.422 R
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116
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117 The third output file:
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118
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119 .. image:: ${static_path}/operation_icons/dwt_var_perClass.png
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120
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121 </help>
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122
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123 </tool>