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1 <tool id="iwtomics_testandplot" name="IWTomics Test" version="@VERSION@.0">
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2 <description>and Plot</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
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11 regionids='${regionids}'
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12 featureids='${featureids}'
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13 rdatafile='${rdata}'
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14
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15 #set region1 = ','.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
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16 #set region2 = ','.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
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17 region1='c(${region1})'
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18 region2='c(${region2})'
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19
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20 features_subset='c(${featureslist})'
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21
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22 statistics="'${conditionalstatistics.statistics}'"
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23 #if $conditionalstatistics.statistics == "quantile":
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24 #set probabilities = ','.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
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25 testprobs='c(${probabilities})'
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26 #end if
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27
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28 B='${permutations}'
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29
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30 testalpha='${plotres.alpha}'
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31 average='${plotres.average}'
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32 size='${plotres.size}'
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33 plottype="'${plotres.conditionalplottype.plottype}'"
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34 #if $plotres.conditionalplottype.plottype == "boxplot":
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35 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
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36 #if $probs != "":
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37 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
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38 #else:
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39 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
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40 #end if
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41 #end if
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42
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43 groupby="'${plotsum.conditionalgroupby.groupby}'"
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44 #if $plotsum.conditionalgroupby.groupby == "test":
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45 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
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46 only_significant='${plotsum.conditionalgroupby.testonlysig}'
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47 #elif $plotsum.conditionalgroupby.groupby == "feature":
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48 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
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49 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
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50 #end if
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51 ]]>
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52 </command>
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53
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54 <inputs>
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55 <!-- RData -->
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56 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
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57 <!-- region IDs -->
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58 <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
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59 <!-- feature IDs -->
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60 <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
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61
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62 <!-- repeat region ids -->
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63 <section name="regionssection" title="Select regions for Interval-Wise Testing" expanded="True" help="IDs of the region datasets to be tested.">
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64 <repeat name="regions" title="Two-sample test" min="1">
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65 <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
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66 <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
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67 </repeat>
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68 </section>
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69
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70 <!-- feature ids list -->
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71 <param name="featureslist" type="data_column" data_ref="featureids" numerical="False" label="Select features" multiple="True" use_header_names="True" help="IDs of the features to be tested." />
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72
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73 <!-- conditional statistics -->
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74 <conditional name="conditionalstatistics">
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75 <!-- statistics -->
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76 <param name="statistics" type="select" label="Test statistics">
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77 <option value="mean">Mean difference</option>
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78 <option value="median">Median difference</option>
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79 <option value="variance">Variance ratio</option>
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80 <option value="quantile">Quantile difference(s)</option>
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81 </param>
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82 <!-- conditional choice: statistics=quantile -->
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83 <when value="quantile">
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84 <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
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85 <repeat name="qprobabilities" title="Probabilities" min="1">
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86 <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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87 </repeat>
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88 </section>
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89 </when>
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90 </conditional>
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91
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92 <!-- permutations -->
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93 <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
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94
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95 <!-- plot IWTomics results -->
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96 <section name="plotres" title="Plot IWTomics test results" expanded="True">
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97 <!-- alpha -->
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98 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
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99 <expand macro="plot-params" />
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100 </section>
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101
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102 <!-- summary plot -->
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103 <expand macro="plot-sum" />
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104 </inputs>
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105
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106 <outputs>
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107 <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
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108 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
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109 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
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110 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
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111 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
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112 <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
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113 </outputs>
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114
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115 <tests>
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116 <test>
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117 <param name="rdata" value="output_loadandplot/iwtomics.loadandplot.RData" ftype="rdata" />
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118 <param name="regionids" value="output_loadandplot/iwtomics.loadandplot.regions.txt" ftype="tabular" />
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119 <param name="featureids" value="output_loadandplot/iwtomics.loadandplot.features.txt" ftype="tabular" />
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120 <repeat name="regions">
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121 <param name="region0" value="2" />
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122 <param name="region1" value="1" />
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123 </repeat>
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124 <repeat name="regions">
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125 <param name="region0" value="3" />
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126 <param name="region1" value="1" />
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127 </repeat>
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128 <repeat name="regions">
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129 <param name="region0" value="4" />
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130 <param name="region1" value="1" />
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131 </repeat>
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132 <param name="featureslist" value="1,2" />
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133 <param name="statistics" value="mean" />
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134 <param name="permutations" value="1000" />
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135 <param name="alpha" value="0.05" />
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136 <param name="average" value="TRUE" />
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137 <param name="size" value="TRUE" />
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138 <param name="plottype" value="boxplot" />
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139 <param name="prob0" value="0.25" />
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140 <param name="prob1" value="0.5" />
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141 <param name="prob2" value="0.75" />
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142 <param name="groupby" value="feature" />
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143 <param name="featurealphaplot" value="0.05" />
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144 <param name="featureonlysig" value="TRUE" />
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145 <output name="adjustedpvaluematrix" file="output_testandplot/iwtomics.testandplot.adjustedpvalue.matrix.txt" compare="sim_size" />
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146 <output name="iwtomicsrespdf" file="output_testandplot/iwtomics.testandplot.iwtomicstestresults.pdf" compare="sim_size" />
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147 <output name="iwtomicssumpdf" file="output_testandplot/iwtomics.testandplot.summaryplot.pdf" compare="sim_size" />
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148 <output name="iwtomicsrdata" file="output_testandplot/iwtomics.testandplot.RData" compare="sim_size" />
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149 <output name="iwtomicstests" file="output_testandplot/iwtomics.testandplot.tests.txt" />
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150 <output name="iwtomicsselectedfeatures" file="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" />
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151 </test>
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152 </tests>
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153
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154 <help><![CDATA[
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155 This tool statistically evaluates differences in genomic features between groups of regions along the genome.
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156 In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
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157 Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
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158 tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
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159 and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
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160 and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*
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161 permits to select the scale to be used in the plots.
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162
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163 -----
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164
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165 **Input files**
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166
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167 RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
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168 These files are created by the tool *IWTomics Load Smooth and Plot*.
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169
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170 -----
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171
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172 **Output**
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173
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174 The tool returns:
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175
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176 1. 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;
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177 2. PDF file with the plotted test results;
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178 3. PDF file with the summary plot;
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179 4. RData with the IWTomicsData object with the test results;
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180 5. Test identifiers;
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181 6. Feature identifiers.
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182
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183 4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
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184
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185 -----
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186
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187 .. class:: infomark
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188
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189 **Notes**
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190
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191 This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
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192
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193 It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
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194 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
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195
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196 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
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197 ]]></help>
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198
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199 <expand macro="citations" />
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200
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201 </tool>
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