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1 id: iwtomics_galaxy
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2 name: IWTomics Tour
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3 description: An interactive tour for the Interval-Wise Testing for omics data (IWTomics) tool for Galaxy
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4 title_default: "Welcome to IWTomics"
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5
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6 steps:
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7 - title: "Welcome to IWTomics"
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8 content: "IWTomics is a tool to statistically evaluate differences in genomic features between groups of regions along the genome. This tour will guide you through a real data example. Please follow the instructions (interaction is required)."
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9 backdrop: true
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10
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11 ######################
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12 ## load ETn example ##
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13 ######################
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14
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15 - title: "Upload data"
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16 element: ".upload-button"
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17 intro: "Upload BED files with the groups of regions to be compared, and TXT files with the corresponding genomic feature measurements."
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18 position: "right"
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19 postclick:
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20 - ".upload-button"
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21 - "#btn-new"
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22
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23 - title: "Upload data"
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24 element: ".upload-text-content:first"
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25 intro: "ETn example: real data from Campos-Sànchez et al. (2016). Upload 'Fixed ETn' and 'Control' regions, as well as 'Recombination Hotspot' content."
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26 position: "top"
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27 textinsert: |
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28 https://raw.githubusercontent.com/fabio-cumbo/IWTomics4Galaxy/master/ETn_example/DESCRIPTION.txt
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29 https://raw.githubusercontent.com/fabio-cumbo/IWTomics4Galaxy/master/ETn_example/ETn_fixed.bed
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30 https://raw.githubusercontent.com/fabio-cumbo/IWTomics4Galaxy/master/ETn_example/Control.bed
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31 https://raw.githubusercontent.com/fabio-cumbo/IWTomics4Galaxy/master/ETn_example/Recombination_hotspots.txt
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32
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33 - title: "Select automatic file type"
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34 element: ".upload-extension:first"
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35 intro: "INTERACTION REQUIRED: Select 'Auto-detect' type, then click 'Next'."
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36 position: "top"
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37 # does not work: let the user select the 'tabular' data type for headers
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38 #textinsert: "tabular"
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39
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40 - title: "Start uploading data"
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41 element: "#btn-start"
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42 intro: "Upload files into Galaxy history."
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43 position: "top"
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44 postclick:
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45 - "#btn-start"
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46
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47 - title: "Wait"
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48 element: ".upload-text-content:first"
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49 intro: "Wait until this block is green, then click 'Next'."
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50 position: "bottom"
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51 postclick:
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52 - "#btn-reset"
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53 - "#btn-new"
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54
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55 - title: "Upload data"
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56 element: ".upload-text-content:first"
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57 intro: "ETn example: real data from Campos-Sànchez et al. (2016). Upload header files for regions and features."
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58 position: "top"
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59 textinsert: |
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60 https://raw.githubusercontent.com/fabio-cumbo/IWTomics4Galaxy/master/ETn_example/regions_header.tabular
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61 https://raw.githubusercontent.com/fabio-cumbo/IWTomics4Galaxy/master/ETn_example/features_header.tabular
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62
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63 - title: "Select header file type"
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64 element: ".upload-extension:first"
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65 intro: "INTERACTION REQUIRED: Select 'tabular' type, then click 'Next'."
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66 position: "top"
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67 # does not work: let the user select the 'tabular' data type for headers
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68 #textinsert: "tabular"
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69
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70 - title: "Start uploading header files"
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71 element: "#btn-start"
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72 intro: "Upload files into Galaxy history."
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73 position: "top"
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74 postclick:
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75 - "#btn-start"
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76
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77 - title: "Close upload/download manager"
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78 element: "#btn-close"
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79 intro: "Close the upload manager with this button or with a click outside of the manager window."
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80 position: "top"
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81 postclick:
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82 - "#btn-close"
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83
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84 - title: "Description File"
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85 element: "#current-history-panel .list-item:eq(5)"
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86 intro: "DESCRIPTION.txt contains a description of the ETn dataset. Click on the eye symbol to inspect it."
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87 position: "left"
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88
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89 - title: "Fixed ETn Regions"
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90 element: "#current-history-panel .list-item:eq(4)"
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91 intro: "ETn_fixed.bed contains genomic coordinates of 1296 64-kb regions flanking fixed ETn elements (elements of the Early Transposon family of active Endogenous Retroviruses in mouse). Click on the eye symbol to inspect it."
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92 position: "left"
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93
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94 - title: "Control Regions"
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95 element: "#current-history-panel .list-item:eq(3)"
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96 intro: "Control.bed contains genomic coordinates of 1142 64-kb regions that do not overlap ETn flanking regions. Click on the eye symbol to inspect it."
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97 position: "left"
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98
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99 - title: "Recombination Hotspot Content"
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100 element: "#current-history-panel .list-item:eq(2)"
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101 intro: "Recombination_hotspots.txt contains genomic coordinates of 2438 64-kb regions (Fixed ETn and Control regions) and, for each of them, the recombination hotspot content measured in 64 1-kb windows. Click on the eye symbol to inspect it."
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102 position: "left"
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103
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104 - title: "Region Header"
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105 element: "#current-history-panel .list-item:eq(1)"
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106 intro: "regions.header contains an identifier for each region dataset and the name to be used in the output. Click on the eye symbol to inspect it."
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107 position: "left"
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108
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109 - title: "Feature Header"
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110 element: "#current-history-panel .list-item:eq(0)"
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111 intro: "features.header contains an identifier for each feature and the name to be used in the output. Click on the eye symbol to inspect it."
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112 position: "left"
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113
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114 - title: "Search for the IWTomics suite"
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115 element: "#tool-search-query"
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116 intro: "INTERACTION REQUIRED: Write 'IWTomics' in the search field. The IWTomics suite contains three tools: 'Load, Smooth and Plot', 'Test and Plot', and 'Plot with Threshold on Test Scale'. Those tools should be used sequentially. Click 'Next' to continue the tour."
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117 position: "right"
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118
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119 #####################################
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120 ## start Load Smooth and Plot tool ##
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121 #####################################
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122
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123 - title: "Select 'Load, Smooth and Plot' tool"
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124 element: 'a[href$="tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_loadandplot%2Fiwtomics_loadandplot%2F1.0.0.0"]'
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125 intro: "Select the first tool 'Load, Smooth and Plot'."
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126 position: "right"
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127 postclick:
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128 - 'a[href$="tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_loadandplot%2Fiwtomics_loadandplot%2F1.0.0.0"]'
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129
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130 - title: "'Load, Smooth and Plot' tool"
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131 content: "'Load, Smooth and Plot' tool imports the genomic region datasets and the corresponding feature measurements."
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132 backdrop: true
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133
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134 - title: "Select region datasets"
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135 element: 'div[tour_id$="regions"]'
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136 intro: "INTERACTION REQUIRED: select the two region datasets 'ETn_fixed.bed' and 'Control.bed', then click 'Next'."
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137 position: "bottom"
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138 # does not work: let the user select the input
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139 #preclick:
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140 #- >-
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141 #div[tour_id$="regions"] > div[class$="ui-form-field"] >
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142 #div[class$="ui-select-content"] > div[class$="ui-select"] >
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143 #select[class$="select"] > option:eq(3)
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144 #- >-
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145 #div[tour_id$="regions"] > div[class$="ui-form-field"] >
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146 #div[class$="ui-select-content"] > div[class$="ui-select"] >
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147 #select[class$="select"] > option:eq(4)
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148
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149 - title: "Select region header"
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150 element: 'div[tour_id$="regionsheader"]'
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151 intro: "INTERACTION REQUIRED: select the region header file 'regions_header.tabular', then click 'Next'."
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152 position: "bottom"
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153 # does not work: let the user select the input
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154 #preclick:
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155 #- 'div[tour_id$="regionsheader"] ul[role$="listbox"] li:eq(3)' # oppure 2 se 'Nothing selected' non conta
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156
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157 - title: "Select feature datasets"
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158 element: 'div[tour_id$="features"]'
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159 intro: "INTERACTION REQUIRED: select the feature file 'Recombination_hotspot.txt', then click 'Next'."
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160 position: "bottom"
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161 # does not work: let the user select the input
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162 #preclick:
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163 #- >-
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164 #div[tour_id$="features"] > div[class$="ui-form-field"] >
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165 #div[class$="ui-select-content"] > div[class$="ui-select"] >
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166 #select[class$="select"] > option:eq(1)
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167
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168 - title: "Select feature header"
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169 element: 'div[tour_id$="featuresheader"]'
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170 intro: "INTERACTION REQUIRED: select the feature header file 'features_header.tabular', then click 'Next'"
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171 position: "top"
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172 # does not work: let the user select the input
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173 #preclick:
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174 #- 'div[tour_id$="featuresheader"] ul[role$="listbox"] li:eq(1)' # oppure 0 se 'Nothing selected' non conta
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175
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176 - title: "Select start positions"
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177 element: 'div[tour_id$="zerobased"]'
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178 intro: "Start positions are 0-based in this example."
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179 position: "top"
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180
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181 - title: "Select smoothing"
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182 element: 'div[tour_id$="conditionaltype|smoothing"]'
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183 intro: "Select the type of smoothing to be applied to the feature curves. Default is 'No' smoothing. Other choices include 'Local Polynomials', 'Gaussian Kernel', and 'B-Splines'."
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184 position: "top"
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185
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186 - title: "Select region alignment"
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187 element: 'div[tour_id$="conditionaltype|alignment"]'
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188 intro: "Select region alignment. Default is 'Center', that alignes regions on their central position. Other choices include 'Left', 'Right', and 'Scale' alignments ('Scale' can only be used if smoothing is applied). In this example all regions have the same length, so the four alignment types are equivalent."
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189 position: "top"
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190
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191 - title: "Plot the mean curves"
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192 element: 'div[tour_id$="plotres|average"]'
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193 intro: "If 'Yes' is selected, a mean feature curve is plotted for each region dataset."
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194 position: "top"
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195
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196 - title: "Plot sample size in each position"
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197 element: 'div[tour_id$="plotres|size"]'
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198 intro: "If 'Yes' is selected, an heatmap with the sample size in each position is plotted for each region dataset."
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199 position: "top"
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200
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201 - title: "Select plot type"
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202 element: 'div[tour_id$="plotres|conditionalplottype|plottype"]'
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203 intro: "Select the graphical representation type: 'Pointwise quantile curves (boxplot)' or 'Curves (aligned)'. In this example we draw a pointwise boxplot."
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204 position: "top"
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205
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206 - title: "Select probabilities"
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207 element: 'div[tour_id$="plotres|conditionalplottype|probabilitiessection|prob0"]'
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208 intro: "Select the probabilities corresponding to the quantile curves to be drawn. Default option is 0.25, 0.50, and 0.75."
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209 position: "top"
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210
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211 - title: "Execute 'Load, Smooth and Plot' tool"
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212 element: '#execute'
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213 intro: "Execute the tool."
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214 position: "right"
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215 postclick:
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216 - '#execute'
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217
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218 - title: "Wait"
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219 content: "Wait until the results are created, then click 'Next'."
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220 backdrop: true
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221
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222 - title: "IWTomicsData Object"
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223 element: "#current-history-panel .list-item:eq(3)"
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224 intro: "This is an RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements."
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225 position: "left"
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226
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227 - title: "Region Dataset IDs"
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228 element: "#current-history-panel .list-item:eq(2)"
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229 intro: "Region Dataset IDs contains the region datasets identifiers. Click on the eye symbol to inspect it."
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230 position: "left"
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231
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232 - title: "Feature IDs"
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233 element: "#current-history-panel .list-item:eq(1)"
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234 intro: "Feature IDs contains the feature identifiers. Click on the eye symbol to inspect it."
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235 position: "left"
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236
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237 - title: "Plotted Data"
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238 element: "#current-history-panel .list-item:eq(0)"
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239 intro: "Plotted Data is a PDF with the pointwise boxplots. Click on the eye symbol to inspect it."
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240 position: "left"
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241
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242 - title: "'Load, Smooth and Plot' completed"
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243 content: "The 'Load, Smooth and Plot' tool demonstration is completed. Click 'Next' to continue with the tool 'Test and Plot'."
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244 backdrop: true
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245
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246 ##############################
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247 ## start Test and Plot tool ##
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248 ##############################
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249
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250 - title: "Select 'Test and Plot' tool"
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251 element: 'a[href$="tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_testandplot%2Fiwtomics_testandplot%2F1.0.0.0"]'
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252 intro: "Select 'Test and Plot' tool."
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253 position: "right"
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254 postclick:
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255 - 'a[href$="tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_testandplot%2Fiwtomics_testandplot%2F1.0.0.0"]'
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256
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257 - title: "'Test and Plot' tool"
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258 content: "'Test and Plot' tool statistically evaluates differences in feature measurements between pairs of genomic region datasets. In particular, it implements the Interval-Wise Testing for omics data."
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259 backdrop: true
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260
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261 - title: "Select IWTomicsData object"
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262 element: 'div[tour_id$="rdata"]'
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263 intro: "INTERACTION REQUIRED: select the IWTomicsData Object created by 'Load, Smooth and Plot' tool, then click 'Next'."
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264 position: "bottom"
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265
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266 - title: "Select region dataset IDs"
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267 element: 'div[tour_id$="regionids"]'
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268 intro: "INTERACTION REQUIRED: select the Region Dataset IDs created by 'Load, Smooth and Plot' tool, then click 'Next'."
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269 position: "bottom"
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270
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271 - title: "Select feature IDs"
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272 element: 'div[tour_id$="featureids"]'
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273 intro: "INTERACTION REQUIRED: select the Feature IDs created by 'Load, Smooth and Plot' tool, then click 'Next'."
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274 position: "bottom"
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275
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276 - title: "Select regions for Interval-Wise Testing"
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277 element: 'div[tour_id$="regionssection|regions_0|region0"]'
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278 intro: "INTERACTION REQUIRED: select pairs of genomic region datasets to be compared using two-sample Interval-Wise Testing. In this example we consider one two-sample test contrasting 'ETn_fixed' (select it as 'Region 1') to 'Control' (select it as 'Region 2'), then click 'Next'."
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279 position: "top"
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280
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281 - title: "Select features"
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282 element: 'div[tour_id$="featureslist"]'
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283 intro: "INTERACTION REQUIRED: select feature measurements to be tested. In this example, select 'Recomb_hot' feature, then click 'Next'."
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284 position: "top"
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285
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286 - title: "Select test statistics"
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287 element: 'div[tour_id$="conditionalstatistics|statistics"]'
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288 intro: "Select the test statistics to be employed in the test. Default is 'Mean difference'. Other choices are 'Median difference', 'Variance ratio', and 'Quantile difference(s)'."
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289 position: "top"
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290
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291 - title: "Select number of permutations"
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292 element: 'div[tour_id$="permutations"]'
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293 intro: "Select number of permutations to be used to compute p-values."
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294 position: "top"
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295
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296 - title: "Select alpha"
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297 element: 'div[tour_id$="plotres|alpha"]'
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298 intro: "Select the level alpha of the test (significance level of the test)."
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299 position: "top"
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300
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301 - title: "Plot the mean curves"
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302 element: 'div[tour_id$="plotres|average"]'
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303 intro: "If 'Yes' is selected, a mean feature curve is plotted for each region dataset."
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304 position: "top"
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305
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306 - title: "Plot sample size in each position"
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307 element: 'div[tour_id$="plotres|size"]'
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308 intro: "If 'Yes' is selected, an heatmap with the sample size in each position is plotted for each region dataset."
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309 position: "top"
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310
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311 - title: "Select plot type"
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312 element: 'div[tour_id$="plotres|conditionalplottype|plottype"]'
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313 intro: "Select the graphical representation type: 'Pointwise quantile curves (boxplot)' or 'Curves (aligned)'. In this example we draw a pointwise boxplot."
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314 position: "top"
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315
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316 - title: "Select probabilities"
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317 element: 'div[tour_id$="plotres|conditionalplottype|probabilitiessection|prob0"]'
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318 intro: "Select the probabilities corresponding to the quantile curves to be drawn. Default option is 0.25, 0.50, and 0.75."
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319 position: "top"
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320
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321 - title: "Select summary plot"
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322 element: 'div[tour_id$="plotsum|conditionalgroupby|groupby"]'
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323 intro: "Select the summary plot to be drawn. Default is 'No plot'. Other choices are a summary plot for each test ('Group by test') and a summary plot for each feature ('Group by feature'). In this example we are performing only one test on one feature, so we select 'No plot'."
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324 position: "top"
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325
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326 - title: "Execute 'Test and Plot' tool"
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327 element: '#execute'
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328 intro: "Execute the tool."
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329 position: "right"
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330 postclick:
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331 - '#execute'
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332
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333 - title: "Wait"
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334 content: "Wait until the results are created, then click 'Next'."
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335 backdrop: true
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336
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337 - title: "Adjusted p-value Matrix"
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338 element: "#current-history-panel .list-item:eq(5)"
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339 intro: "This is a TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test. Click on the eye symbol to inspect it."
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340 position: "left"
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341
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342 - title: "Plotted Test Results"
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343 element: "#current-history-panel .list-item:eq(4)"
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344 intro: "Plotted Test Results is a PDF file with the plotted test results. Click on the eye symbol to inspect it."
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345 position: "left"
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346
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347 - title: "Summary Plot"
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348 element: "#current-history-panel .list-item:eq(3)"
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349 intro: "If a summary plot was selected in 'Test and Plot' tool, this is a PDF file with the summary plot. If 'No plot' was selected, this is empty."
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350 position: "left"
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351
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352 - title: "IWTomicsData Object with Test Results"
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353 element: "#current-history-panel .list-item:eq(2)"
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354 intro: "This is an RData with the IWTomicsData Object with the test results."
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355 position: "left"
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356
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357 - title: "Test IDs"
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358 element: "#current-history-panel .list-item:eq(1)"
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359 intro: "Test IDs contains the test identifiers. Click on the eye symbol to inspect it."
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360 position: "left"
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361
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362 - title: "Feature IDs"
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363 element: "#current-history-panel .list-item:eq(0)"
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364 intro: "Feature IDs contains the feature identifiers. Click on the eye symbol to inspect it."
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365 position: "left"
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366
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367 - title: "'Test and Plot' completed"
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368 content: "The 'Test and Plot' tool demonstration is completed. Click 'Next' to continue with the tool 'Plot with Threshold on Test Scale'."
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369 backdrop: true
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370
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371 #############################################
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372 ## start Plot with Threshold on Test Scale ##
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373 #############################################
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374
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375 - title: "Select 'Plot with Threshold on Test Scale' tool"
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376 element: 'a[href$="tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_plotwithscale%2Fiwtomics_plotwithscale%2F1.0.0.0"]'
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377 intro: "Select 'Plot with Threshold on Test Scale' tool."
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378 position: "right"
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379 postclick:
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380 - 'a[href$="tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiwtomics_plotwithscale%2Fiwtomics_plotwithscale%2F1.0.0.0"]'
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381
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382 - title: "'Plot with Threshold on Test Scale' tool"
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383 content: "'Plot with Threshold on Test Scale' tool allows to select the scale for the Interval-Wise Testing results."
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384 backdrop: true
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385
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386 - title: "Select IWTomicsData object with test results"
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387 element: 'div[tour_id$="rdata"]'
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388 intro: "INTERACTION REQUIRED: select the IWTomicsData Object with Test Results created by 'Test and Plot' tool, then click 'Next'."
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389 position: "bottom"
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390
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391 - title: "Select test IDs"
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392 element: 'div[tour_id$="testids"]'
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393 intro: "INTERACTION REQUIRED: select the Test IDs created by 'Test and Plot' tool, then click 'Next'."
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394 position: "bottom"
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395
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396 - title: "Select feature IDs"
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397 element: 'div[tour_id$="featureids"]'
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398 intro: "INTERACTION REQUIRED: select the Feature IDs created by 'Test and Plot' tool, then click 'Next'."
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399 position: "bottom"
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400
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401 - title: "Select scale"
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402 element: 'div[tour_id$="scalesection|thresholdontestscale_0|test"]'
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403 intro: "INTERACTION REQUIRED: select the scale to be used in Interval-Wise Testing results and plot. First, select the test identifier 'ETn_fixed vs Control', then click 'Next'."
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404 position: "top"
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405
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406 - title: "Select scale"
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407 element: 'div[tour_id$="scalesection|thresholdontestscale_0|feature"]'
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408 intro: "INTERACTION REQUIRED: select the feature identifier 'Recomb_hot', then click 'Next'."
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409 position: "top"
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410
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411 - title: "Select scale"
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412 element: 'div[tour_id$="scalesection|thresholdontestscale_0|scale"]'
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413 intro: "INTERACTION REQUIRED: select the scale '8' (8-kb scale) for the test and feature selected above, then click 'Next'."
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414 position: "top"
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415
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416 - title: "Select alpha"
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417 element: 'div[tour_id$="plotres|alpha"]'
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418 intro: "Select the level alpha of the test (significance level of the test)."
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419 position: "top"
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420
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421 - title: "Plot the mean curves"
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422 element: 'div[tour_id$="plotres|average"]'
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423 intro: "If 'Yes' is selected, a mean feature curve is plotted for each region dataset."
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424 position: "top"
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425
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426 - title: "Plot sample size in each position"
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427 element: 'div[tour_id$="plotres|size"]'
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428 intro: "If 'Yes' is selected, an heatmap with the sample size in each position is plotted for each region dataset."
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429 position: "top"
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430
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431 - title: "Select plot type"
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432 element: 'div[tour_id$="plotres|conditionalplottype|plottype"]'
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433 intro: "Select the graphical representation type: 'Pointwise quantile curves (boxplot)' or 'Curves (aligned)'. In this example we draw a pointwise boxplot."
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434 position: "top"
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435
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436 - title: "Select probabilities"
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437 element: 'div[tour_id$="plotres|conditionalplottype|probabilitiessection|prob0"]'
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438 intro: "Select the probabilities corresponding to the quantile curves to be drawn. Default option is 0.25, 0.50, and 0.75."
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439 position: "top"
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440
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441 - title: "Select summary plot"
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442 element: 'div[tour_id$="plotsum|conditionalgroupby|groupby"]'
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443 intro: "Select the summary plot to be drawn. Default is 'No plot'. Other choices are a summary plot for each test ('Group by test') and a summary plot for each feature ('Group by feature'). In this example we are performing only one test on one feature, so we select 'No plot'."
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444 position: "top"
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445
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446 - title: "Execute 'Plot with Threshold on Test Scale' tool"
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447 element: '#execute'
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448 intro: "Execute the tool."
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449 position: "right"
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450 postclick:
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451 - '#execute'
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452
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453 - title: "Wait"
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454 content: "Wait until the results are created, then click 'Next'."
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455 backdrop: true
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456
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457 - title: "Adjusted p-value"
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458 element: "#current-history-panel .list-item:eq(2)"
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459 intro: "This is a TXT file with an adjusted p-value curve for every test performed at the selected scale. Click on the eye symbol to inspect it."
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460 position: "left"
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461
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462 - title: "Plotted Test Results"
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463 element: "#current-history-panel .list-item:eq(1)"
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464 intro: "Plotted Test Results is a PDF file with the plotted test results, at the selected scale. Click on the eye symbol to inspect it."
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465 position: "left"
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466
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467 - title: "Summary Plot"
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468 element: "#current-history-panel .list-item:eq(0)"
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469 intro: "If a summary plot was selected in 'Test and Plot' tool, this is a PDF file with the summary plot. If 'No plot' was selected, this is empty."
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470 position: "left"
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471
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472 - title: "End of the tour"
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473 content: "IWTomics tour is completed. Enjoy!"
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474 backdrop: true
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