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1 <tool id="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 <stdio>
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8 <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
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9 <exit_code range="10" source="both" level="fatal" description="Wrong region ids." />
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10 <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
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11 <exit_code range="30" source="both" level="fatal" description="Same test repeated multiple times." />
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12 <exit_code range="40" source="both" level="fatal" description="Testing error." />
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13 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
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14 </stdio>
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15
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16 <command>
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17 <![CDATA[
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18 Rscript $__tool_directory__/testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}"
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19 regionids="${regionids}"
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20 featureids="${featureids}"
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21 rdatafile="${rdata}"
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22
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23 #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
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24 #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
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25 region1="c(${region1})"
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26 region2="c(${region2})"
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27
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28 features_subset="c(${featureslist})"
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29
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30 statistics="'${conditionalstatistics.statistics}'"
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31 #if $conditionalstatistics.statistics == "quantile":
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32 #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
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33 testprobs="c(${probabilities})"
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34 #end if
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35
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36 B="${permutations}"
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37
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38 testalpha="${plotres.alpha}"
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39 average="${plotres.average}"
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40 size="${plotres.size}"
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41 plottype="'${plotres.conditionalplottype.plottype}'"
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42 #if $plotres.conditionalplottype.plottype == 'boxplot':
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43 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
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44 #if $probs != "":
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45 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
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46 #else:
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47 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
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48 #end if
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49 #end if
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50
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51 groupby="'${plotsum.conditionalgroupby.groupby}'"
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52 #if $plotsum.conditionalgroupby.groupby == "test":
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53 summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
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54 only_significant="${plotsum.conditionalgroupby.testonlysig}"
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55 #elif $plotsum.conditionalgroupby.groupby == "feature":
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56 summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
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57 only_significant="${plotsum.conditionalgroupby.featureonlysig}"
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58 #end if
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59
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60 >& /dev/null
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61 ]]>
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62 <!--
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63 to print the stack add the following line at the end of the command and enable the corresponding entry in output
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64 2> "${stackerr}"
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65 -->
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66 </command>
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67
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68 <inputs>
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69 <!-- RData -->
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70 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
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71 <!-- region IDs -->
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72 <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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73 <!-- feature IDs -->
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74 <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
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75
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76 <!-- repeat region ids -->
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77 <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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78 <repeat name="regions" title="Two-sample test" min="1">
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79 <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
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80 <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
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81 </repeat>
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82 </section>
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83
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84 <!-- feature ids list -->
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85 <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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86
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87 <!-- conditional statistics -->
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88 <conditional name="conditionalstatistics">
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89 <!-- statistics -->
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90 <param name="statistics" type="select" label="Test statistics">
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91 <option value="mean">Mean difference</option>
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92 <option value="median">Median difference</option>
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93 <option value="variance">Variance ratio</option>
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94 <option value="quantile">Quantile difference(s)</option>
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95 </param>
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96 <!-- conditional choice: statistics=quantile -->
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97 <when value="quantile">
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98 <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
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99 <repeat name="qprobabilities" title="Probabilities" min="1">
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100 <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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101 </repeat>
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102 </section>
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103 </when>
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104 </conditional>
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105
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106 <!-- permutations -->
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107 <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
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108
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109 <!-- plot IWTomics results -->
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110 <section name="plotres" title="Plot IWTomics test results" expanded="True">
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111 <!-- alpha -->
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112 <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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113 <!-- average -->
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114 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
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115 <!-- average -->
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116 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
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117 <!-- conditional plot type -->
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118 <conditional name="conditionalplottype">
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119 <!-- plot type -->
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120 <param name="plottype" type="select" label="Plot type">
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121 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
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122 <option value="curves">Curves (aligned)</option>
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123 </param>
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124 <!-- conditional choice: plottype=boxplot -->
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125 <when value="boxplot">
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126 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
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127 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
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128 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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129 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
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130 <repeat name="probabilities" title="Probabilities">
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131 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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132 </repeat>
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133 </section>
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134 </when>
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135 </conditional>
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136 </section>
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137
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138 <!-- summary plot -->
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139 <section name="plotsum" title="Summary plot" expanded="True">
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140 <!-- conditional group by -->
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141 <conditional name="conditionalgroupby">
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142 <!-- group by -->
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143 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
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144 <option value="none">No plot</option>
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145 <option value="test">Group by test</option>
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146 <option value="feature">Group by feature</option>
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147 </param>
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148 <when value="test">
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149 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
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150 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
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151 </when>
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152 <when value="feature">
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153 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
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154 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
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155 </when>
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156 </conditional>
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157 </section>
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158 </inputs>
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159
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160 <outputs>
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161 <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
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162 <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
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163 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
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164 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
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165 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
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166 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
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167 <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
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168 </outputs>
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169
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170 <help>
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171 This tool statistically evaluates differences in genomic features between groups of regions along the genome.
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172 In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
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173 Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
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174 tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
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175 and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
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176 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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177 permits to select the scale to be used in the plots.
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178
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179 -----
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180
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181 **Input files**
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182
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183 RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
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184 These files are created by the tool *IWTomics Load Smooth and Plot*.
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185
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186 -----
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187
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188 **Output**
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189
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190 The tool returns:
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191
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192 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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193 2. PDF file with the plotted test results;
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194 3. PDF file with the summary plot;
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195 4. RData with the IWTomicsData object with the test results;
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196 5. Test identifiers;
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197 6. Feature identifiers.
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198
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199 4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
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200
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201 -----
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202
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203 .. class:: infomark
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204
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205 **Notes**
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206
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207 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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208
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209 It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
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210 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
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211
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212 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
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213 </help>
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214
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215 <citations>
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216 <citation type="bibtex">
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217 @ARTICLE{
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218 iwt-functional-data,
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219 author = {A Pini and S. Vantini},
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220 title = {Interval-Wise Testing for functional data},
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221 journal = {Journal of Nonparametric Statistics},
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222 year = {2017},
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223 volume = {29},
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224 number = {2},
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225 pages = {407-424}
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226 }
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227 </citation>
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228 <citation type="bibtex">
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229 @MANUAL{
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230 iwtomics,
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231 author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
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232 title = {IWTomics: Interval-Wise Testing for Omics Data},
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233 note = {R package version 0.99.12},
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234 year = {2017}
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235 }
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236 </citation>
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237 </citations>
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238
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239 </tool>
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