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1 <tool id="iwtomics_plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">
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18
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2 <description>on Test Scale</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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64
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8 <exit_code range="-1" 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" level="fatal" description="Wrong test ids." />
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10 <exit_code range="20" level="fatal" description="Wrong feature ids." />
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11 <exit_code range="30" level="fatal" description="Two scale thresholds selected for the same test and feature." />
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12 <exit_code range="40" level="fatal" description="Scale threshold too high." />
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13 <exit_code range="50" level="fatal" description="Group by 'test' but selected features with different resolution." />
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14 <exit_code range="60" level="fatal" description="Summary plot error. Please try again." />
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15 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
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18
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16 </stdio>
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17
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18 <command>
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19 <![CDATA[
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20 Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
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21 iwtomicsrdata='${rdata}'
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22 iwtomicstests='${testids}'
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23 iwtomicsselectedfeatures='${featureids}'
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24
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25 #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
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26 test_subset='${test_subset}'
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27 #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
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28 feature_subset='${feature_subset}'
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29 #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
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30 scale_subset='c(${scale_subset})'
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31
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32 testalpha='${plotres.alpha}'
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33 average='${plotres.average}'
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34 size='${plotres.size}'
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35 plottype='${plotres.conditionalplottype.plottype}'
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36 #if $plotres.conditionalplottype.plottype == 'boxplot':
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37 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
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38 #if $probs != "":
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39 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
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40 #else:
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41 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
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42 #end if
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43 #end if
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44
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45 groupby='${plotsum.conditionalgroupby.groupby}'
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46 #if $plotsum.conditionalgroupby.groupby == "test":
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47 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
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48 only_significant='${plotsum.conditionalgroupby.testonlysig}'
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49 #elif $plotsum.conditionalgroupby.groupby == "feature":
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50 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
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51 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
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52 #end if
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53
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54 >& /dev/null
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55 ]]>
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56 <!--
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57 to print the stack add the following line at the end of the command and enable the corresponding entry in output
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58 2> "${stackerr}"
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59 -->
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60 </command>
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61
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62 <inputs>
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63 <!-- RData -->
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64 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
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65 <!-- test IDs -->
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66 <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by 'IWTomics Test and Plot'." />
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67 <!-- feature IDs -->
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68 <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Test and Plot'." />
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69
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70 <!-- repeat threshold on test scale -->
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71 <section name="scalesection" title="Select scale for Interval-Wise Testing and plot" expanded="True" help="Maximum interval length for the p-value adjustment. If 0 the maximum possible scale is used.">
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72 <repeat name="thresholdontestscale" title="Threshold on test scale" min="1">
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73 <param name="test" type="data_column" data_ref="testids" numerical="False" label="Test ID" multiple="True" use_header_names="True" />
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74 <param name="feature" type="data_column" data_ref="featureids" numerical="False" label="Feature ID" multiple="True" use_header_names="True" />
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75 <param name="scale" type="integer" value="0" min="0" label="Scale" />
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76 </repeat>
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77 </section>
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78
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79 <!-- plot IWTomics results -->
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80 <section name="plotres" title="Plot IWTomics test results" expanded="True">
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81 <!-- alpha -->
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82 <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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83 <!-- average -->
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84 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
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85 <!-- average -->
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86 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
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87 <!-- conditional plot type -->
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88 <conditional name="conditionalplottype">
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89 <!-- plot type -->
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90 <param name="plottype" type="select" label="Plot type">
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91 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
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92 <option value="curves">Curves (aligned)</option>
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93 </param>
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94 <!-- conditional choice: plottype=boxplot -->
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95 <when value="boxplot">
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96 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
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97 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
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98 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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99 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
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100 <repeat name="probabilities" title="Probabilities">
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101 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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102 </repeat>
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103 </section>
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104 </when>
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105 </conditional>
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106 </section>
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107
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108 <!-- summary plot -->
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109 <section name="plotsum" title="Summary plot" expanded="True">
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110 <!-- conditional group by -->
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111 <conditional name="conditionalgroupby">
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112 <!-- group by -->
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113 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
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114 <option value="none">No plot</option>
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115 <option value="test">Group by test</option>
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116 <option value="feature">Group by feature</option>
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117 </param>
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118 <when value="test">
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119 <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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120 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
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121 </when>
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122 <when value="feature">
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123 <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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124 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
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125 </when>
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126 </conditional>
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127 </section>
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128 </inputs>
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129
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130 <outputs>
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131 <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.plotwithscale.stackerr.txt" />-->
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132 <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
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133 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
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134 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
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135 </outputs>
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136
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137 <tests>
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138 <test>
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139 <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
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140 <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
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141 <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
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142 <repeat name="thresholdontestscale">
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143 <param name="test" value="1" />
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144 <param name="feature" value="1" />
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145 <param name="scale" value="10" />
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146 </repeat>
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147 <repeat name="thresholdontestscale">
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148 <param name="test" value="1,2,3" />
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149 <param name="feature" value="2" />
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150 <param name="scale" value="20" />
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151 </repeat>
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152 <param name="alpha" value="0.05" />
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153 <param name="average" value="TRUE" />
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154 <param name="size" value="TRUE" />
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155 <param name="plottype" value="boxplot" />
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156 <param name="prob0" value="0.25" />
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157 <param name="prob1" value="0.5" />
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158 <param name="prob2" value="0.75" />
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159 <param name="groupby" value="feature" />
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160 <param name="featurealphaplot" value="0.05" />
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161 <param name="featureonlysig" value="TRUE" />
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162 <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
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163 <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
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164 <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
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165 </test>
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166 </tests>
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167
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168 <help><![CDATA[
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169 This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
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170 for the different tests performed at the selected scale, and it creates a graphical representation of the
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171 Interval-Wise Testing results and a summary plot (optional) at the selected scale.
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172
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173 -----
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174
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175 **Input files**
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176
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177 RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.
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178 These files are created by the tool *IWTomics Test and Plot*.
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179
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180 -----
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181
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182 **Output**
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183
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184 The tool returns:
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185
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186 1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
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187 2. PDF file with the plotted test results;
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188 3. PDF file with the summary plot.
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189
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190 -----
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191
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192 .. class:: infomark
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193
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194 **Notes**
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195
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196 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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197
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198 It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
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199 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
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200
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201 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
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202 ]]></help>
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203
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204 <expand macro="citations" />
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205
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206 </tool>
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