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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 18:12:29 +0000
parents 91fad0f30fd3
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509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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1 <tool id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" name="Compute P-values and Second Moments for Feature Occurrences" version="1.0.1">
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2 <description>between two datasets 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 '$__tool_directory__/execute_dwt_IvC_all.R'
509993d9fdca "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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9 '$inputFile1'
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10 '$inputFile2'
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11 '$outputFile2'
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12 '$outputFile1'
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13 </command>
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14 <inputs>
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15 <param format="tabular" name="inputFile1" type="data" label="Select the first input file"/>
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16 <param format="tabular" name="inputFile2" type="data" label="Select the second input file"/>
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="outputFile1" label="${tool.name} on ${on_string}: statistics"/>
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20 <data format="pdf" name="outputFile2" label="${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="inputFile1" value="in1.tsv"/>
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25 <param ftype="tabular" name="inputFile2" value="in2.tsv"/>
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26 <output name="outputFile1" ftype="tabular">
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27 <assert_contents><has_line_matching expression="^motif\t1_moment2.*"/></assert_contents>
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28 <assert_contents><has_line_matching expression="^translinTarget.*" /></assert_contents>
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29 </output>
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30 <output name="outputFile2" ftype="pdf" file="out2.pdf" compare="sim_size"/>
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31 </test>
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32 </tests>
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33 <help>
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34
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35 .. class:: infomark
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36
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37 **What it does**
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38
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39 This program generates plots and computes table matrix of second moments, p-values, and test orientations at multiple scales for the correlation between the occurrences of features in one dataset and their occurrences in another using multiscale wavelet analysis technique.
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40
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41 The program assumes that the user has two sets of DNA sequences, S1 and S1, each of which consists of one or more sequences of equal length. Each sequence in each set 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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42
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43 The program has two input files obtained as follows:
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44
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45 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 S1 and S1, and builds two tabular files representing the count results in each interval of S1 and S1. These are the input files of the program.
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46
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47 The program gives two output files:
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48
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49 - The first output file is a TABULAR format file representing the second moments, p-values, and test orientations for each feature at each scale.
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50 - The second output file is a PDF file consisting of as many figures as the number of features, such that each figure represents the values of the second moment for that feature at every scale.
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51
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52 -----
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53
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54 .. class:: warningmark
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55
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56 **Note**
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57
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58 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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59
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60 -----
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61
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62 **Example**
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63
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64 Counting the occurrences of 5 features (motifs) in 16 intervals (one line per interval) of the DNA sequences in S1 gives the following tabular file::
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65
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66 deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget
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67 226 403 416 221 1165
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68 236 444 380 241 1223
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69 242 496 391 195 1116
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70 243 429 364 191 1118
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71 244 410 371 236 1063
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72 230 386 370 217 1087
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73 275 404 402 214 1044
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74 265 443 365 231 1086
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75 255 390 354 246 1114
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76 281 384 406 232 1102
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77 263 459 369 251 1135
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78 280 433 400 251 1159
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79 278 385 382 231 1147
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80 248 393 389 211 1162
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81 251 403 385 246 1114
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82 239 383 347 227 1172
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83
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84 And counting the occurrences of 5 features (motifs) in 16 intervals (one line per interval) of the DNA sequences in S2 gives the following tabular file::
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85
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86 deletionHoptspot insertionHoptspot dnaPolPauseFrameshift topoisomeraseCleavageSite translinTarget
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87 235 374 407 257 1159
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88 244 356 353 212 1128
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89 233 343 322 204 1110
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90 222 329 398 253 1054
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91 216 325 328 253 1129
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92 257 368 352 221 1115
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93 238 360 346 224 1102
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94 225 350 377 248 1107
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95 230 330 365 236 1132
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96 241 389 357 220 1120
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97 274 354 392 235 1120
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98 250 379 354 210 1102
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99 254 329 320 251 1080
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100 221 355 406 279 1127
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101 224 330 390 249 1129
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102 246 366 364 218 1176
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103
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104
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105 We notice that the number of scales here is 4 because 16 = 2^4. Runnig the program on the above input files gives the following output:
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106
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107 The first output file::
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108
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109 motif 1_moment2 1_pval 1_test 2_moment2 2_pval 2_test 3_moment2 3_pval 3_test 4_moment2 4_pval 4_test
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110
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111 deletionHoptspot 0.8751 0.376 L 1.549 0.168 R 0.6152 0.434 L 0.5735 0.488 R
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112 insertionHoptspot 0.902 0.396 L 1.172 0.332 R 0.6843 0.456 L 1.728 0.213 R
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113 dnaPolPauseFrameshift 1.65 0.013 R 0.267 0.055 L 0.1387 0.124 L 0.4516 0.498 L
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114 topoisomeraseCleavageSite 0.7443 0.233 L 1.023 0.432 R 1.933 0.155 R 1.09 0.3 R
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115 translinTarget 0.5084 0.057 L 0.8219 0.446 L 3.604 0.019 R 0.4377 0.492 L
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116
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117 The second output file:
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118
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119 .. image:: ${static_path}/operation_icons/dwt_IvC_1.png
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120 .. image:: ${static_path}/operation_icons/dwt_IvC_2.png
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121 .. image:: ${static_path}/operation_icons/dwt_IvC_3.png
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122 .. image:: ${static_path}/operation_icons/dwt_IvC_4.png
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123 .. image:: ${static_path}/operation_icons/dwt_IvC_5.png
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124
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125 </help>
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126
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127 </tool>