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1 <tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="15">
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2 <description> Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization. </description>
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3 <macros>
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4 <import>citations.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package">r-biocmanager</requirement>
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8 <requirement type="package">pandoc</requirement>
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9 <requirement type="package">r-base</requirement>
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10 <requirement type="package">r-batch</requirement>
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11 <requirement type="package">bioconductor-affyplm</requirement>
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12 <requirement type="package">bioconductor-affy</requirement>
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13 <requirement type="package">bioconductor-annotate</requirement>
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14 <requirement type="package">r-knitr</requirement>
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15 <requirement type="package">bioconductor-marray</requirement>
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16 <requirement type="package">r-idpmisc</requirement>
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17 <requirement type="package">r-kernsmooth</requirement>
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18 <requirement type="package">r-rmarkdown</requirement>
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19 <requirement type="package">r-markdown</requirement>
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20 <requirement type="package">bioconductor-limma</requirement>
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21 <requirement type="package">r-idpmisc</requirement>
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22 </requirements>
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23 <stdio>
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24 <exit_code range="1:" level="fatal" />
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25 </stdio>
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26 <command>
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27 <![CDATA[
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28 Rscript
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29 #if $technologies.technology == "Affymetrix":
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30 '$__tool_directory__/Affymetrix_Preprocessing.R'
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31 thefunctions "AffymetrixPreprocessingFunction"
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32 image $image
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33 backgroundcorrection_method $technologies.BackgroundCorrectionA
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34 normalization_method $technologies.NormalizationA
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35 summary_method $technologies.SummarizationA
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36 #elif $technologies.technology == "Agilent":
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37 #if $technologies.channelsA.channelA == "one":
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38 '$__tool_directory__/Agilent_One_Color_Preprocessing.R'
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39 thefunction "AgilentOneColorPreprocessingFunction"
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40 image $image
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41 methodBC $technologies.channelsA.BackgroundCorrectionAG
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42 methodNBA $technologies.channelsA.methodNBAAG
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43 #else:
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44 '$__tool_directory__/Agilent_Two_Colors_Preprocessing.R'
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45 thefunction "AgilentTwoChannelsPreprocessingFunction"
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46 image $image
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47 methodBC $technologies.channelsA.BackgroundCorrectionAGT
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48 methodNWA $technologies.channelsA.methodNWAAGT
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49 methodNBA $technologies.channelsA.methodNBAAGT
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50 #end if
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51 #else:
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52 #if $technologies.channelsG.channelG == "one"
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53 '$__tool_directory__/GenePix_One_Color_Preprocessing.R'
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54 thefunction "GenePixOneColorPreprocessingFunction"
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55 image $image
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56 methodBC $technologies.channelsG.BackgroundCorrectionG
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57 methodNBA $technologies.channelsG.methodNBAG
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58 #else:
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59 '$__tool_directory__/GenePix_Two_Colors_Preprocessing.R'
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60 thefunction "GenePixTwoChannelsPreprocessingFunction"
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61 image $image
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62 methodBC $technologies.channelsG.BackgroundCorrectionGT
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63 methodNWA $technologies.channelsG.methodNWAGT
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64 methodNBA $technologies.channelsG.methodNBAGT
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65 #end if
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66 #end if
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67 w $w
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68 h $h
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69 ]]>
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70 </command>
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71 <inputs>
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72 <param name="image" type="data" format="rdata" label="Project microarray as a binary rdata" help="Last output from tool read dataset." >
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73 <validator type="expression" message="Please select output dataset from read dataset tool ">'Read.Project' in value.name</validator>
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74 </param>
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75 <conditional name="technologies">
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76 <param name="technology" type="select" label="Select the technology">
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77 <option value="Affymetrix" selected="true">Affymetrix</option>
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78 <option value="Agilent">Agilent</option>
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79 <option value="GenePix">GenePix</option>
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80 </param>
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81 <when value="Affymetrix">
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82 <param name="BackgroundCorrectionA" type="select" label="Background correction method.">
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83 <option value="mas" selected="true">Mas</option>
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84 <option value="rma">Rma</option>
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85 <option value="none">None</option>
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86 </param>
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87 <param name="NormalizationA" type="select" label="Normalization method.">
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88 <option value="quantiles" selected="true">Quantiles</option>
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89 <option value="quantiles.robust">Quantiles robust</option>
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90 <option value="quantiles.probeset">Quantiles Probeset</option>
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91 <option value="constant">Constant</option>
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92 <option value="contrasts">Contrasts</option>
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93 <option value="invariantset">Invariantset</option>
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94 <option value="loess">Loess</option>
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95 <option value="qspline">QSPline</option>
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96 <option value="scaling">Scaling</option>
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97 <option value="vsn">VSN</option>
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98 </param>
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99 <param name="SummarizationA" type="select" label="Summarization method.">
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100 <option value="median.polish" selected="true">Median.polish</option>
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101 <option value="tukey.biweight">Tukey.biweight</option>
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102 <option value="average.log">Average.log</option>
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103 <option value="log.average">Log.average</option>
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104 <option value="rlm">Rlm</option>
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105 <option value="lm">Lm</option>
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106 <option value="log.median">Log.median</option>
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107 <option value="median.log">Median.log</option>
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108 <option value="log.2nd.largest">Log.2nd.largest</option>
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109 </param>
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110 </when>
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111 <when value="Agilent">
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112 <conditional name="channelsA">
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113 <param name="channelA" type="select" label="Select the number of channels">
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114 <option value="one" selected="true">One</option>
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115 <option value="two">Two</option>
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116 </param>
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117 <when value="one">
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118 <param name="BackgroundCorrectionAG" type="select" label="Background correction method.">
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119 <option value="auto" selected="true">Auto</option>
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120 <option value="none">None</option>
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121 <option value="subtract">Subtract</option>
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122 <option value="half">Half</option>
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123 <option value="minimum">Minimum</option>
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124 <option value="movingmin">MovingMin</option>
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125 <option value="edwards">Edwards</option>
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126 <option value="normexp">NormExp</option>
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127 </param>
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128 <param name="methodNBAAG" type="select" label="Normalization between arrays.">
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129 <option value="scale" selected="true">Scale</option>
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130 <option value="quantile">Quantile</option>
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131 <option value="cyclicloess">CyclicLoess</option>
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132 </param>
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133 </when>
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134 <when value="two">
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135 <param name="BackgroundCorrectionAGT" type="select" label="Background correction method.">
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136 <option value="auto" selected="true">Auto</option>
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137 <option value="none">None</option>
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138 <option value="subtract">Subtract</option>
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139 <option value="half">Half</option>
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140 <option value="minimum">Minimum</option>
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141 <option value="movingmin">MovingMin</option>
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142 <option value="edwards">Edwards</option>
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143 <option value="normexp">NormExp</option>
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144 </param>
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145 <param name="methodNWAAGT" type="select" label="Normalization within arrays.">
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146 <option value="median" selected="true">Median</option>
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147 <option value="loess">Loess</option>
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148 <option value="printtiploess">PrintTiploess</option>
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149 </param>
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150 <param name="methodNBAAGT" type="select" label="Normalization between arrays.">
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151 <option value="scale" selected="true">Scale</option>
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152 <option value="quantile">Quantile</option>
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153 <option value="Aquantile">AQuantile</option>
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154 <option value="cyclicloess">CyclicLoess</option>
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155 </param>
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156 </when>
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157 </conditional>
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158 </when>
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159 <when value="GenePix">
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160 <conditional name="channelsG">
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161 <param name="channelG" type="select" label="Select the number of channels">
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162 <option value="one" selected="true">One</option>
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163 <option value="two">Two</option>
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164 </param>
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165 <when value="one">
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166 <param name="BackgroundCorrectionG" type="select" label="Background correction method.">
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167 <option value="auto" selected="true">Auto</option>
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168 <option value="none">None</option>
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169 <option value="subtract">Subtract</option>
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170 <option value="half">Half</option>
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171 <option value="minimum">Minimum</option>
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172 <option value="movingmin">MovingMin</option>
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173 <option value="edwards">Edwards</option>
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174 <option value="normexp">NormExp</option>
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175 </param>
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176 <param name="methodNBAG" type="select" label="Normalization between arrays.">
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177 <!--<option value="scale" selected="true">Scale</option>-->
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178 <option value="quantile" selected="true">Quantile</option>
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179 <option value="scale">Scale</option>
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180 <option value="cyclicloess">CyclicLoess</option>
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181 </param>
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182 </when>
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183 <when value="two">
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184 <param name="BackgroundCorrectionGT" type="select" label="Background correction method.">
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185 <option value="auto" selected="true">Auto</option>
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186 <option value="none">None</option>
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187 <option value="subtract">Subtract</option>
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188 <option value="half">Half</option>
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189 <option value="minimum">Minimum</option>
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190 <option value="movingmin">MovingMin</option>
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191 <option value="edwards">Edwards</option>
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192 <option value="normexp">NormExp</option>
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193 </param>
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194 <param name="methodNWAGT" type="select" label="Normalization within arrays.">
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195 <option value="median" selected="true">Median</option>
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196 <option value="loess">Loess</option>
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197 <option value="printtiploess">PrintTiploess</option>
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198 </param>
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199 <param name="methodNBAGT" type="select" label="Normalization between arrays.">
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200 <!--<option value="scale" >Scale</option>-->
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201 <option value="quantile" selected="true">Quantile</option>
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202 <option value="scale">Scale</option>
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203 <option value="cyclicloess">CyclicLoess</option>
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204 <option value="Aquantile">AQuantile</option>
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205 </param>
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206 </when>
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207 </conditional>
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208 </when>
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209 </conditional>
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210 <param name="w" type="integer" value="1024" label="Plot's width" />
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211 <param name="h" type="integer" value="1024" label="Plot's height" />
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212 </inputs>
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213 <outputs>
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214 <data name="ProcessDataSetRData" format="rdata" from_work_dir="MicroArray.Preprocessing.RData" label="Preprocess.Project.Data.RData" />
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215 <data name="Matrix.Data" format="tabular" from_work_dir="Matrix.Data.tsv" label="Matrix.Data.tsv" />
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216 <data name="Preprocessing.Plots" format="html" from_work_dir="PreprocessingPlots.html" label="Preprocessing.Plots.html" />
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217 </outputs>
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218 <tests>
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219 <test>
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220 <param name="image" ftype="rdata" value="Read.Project.Data.RData" />
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221 <param name="technologies|technology" value="GenePix"/>
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222 <param name="technologies|channelsG|channelG" value="two"/>
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223 <param name="technologies|channelsG|BackgroundCorrectionGT" value="auto"/>
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224 <param name="technologies|channelsG|methodNWAGT" value="median"/>
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225 <param name="technologies|channelsG|methodNBAGT" value="quantile"/>
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226 <output name="ProcessDataSetRData" ftype="rdata" file="Preprocess.Project.Data.RData" compare="sim_size" >
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227 </output>
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228 <output name="Matrix.Data" ftype="tabular" file="Matrix.Data.tsv" >
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229 </output>
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230 <output name="Preprocessing.Plots" ftype="html" file="Preprocessing.Plots.html" compare="sim_size">
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231 </output>
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232 </test>
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233 </tests>
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234 <help>
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235
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236 .. class:: infomark
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237
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238 **Authors** T.Bensellak, B.Ettetuani.
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239
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240 ---------------------------------------------------
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241
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242 ==================================
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243 Preprocessing Microarray DataSet
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244 ==================================
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245
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246 -----------
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247 Description
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248 -----------
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249
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250 This tool is used as first phase of the global workflow, the preprocessing .
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251
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252 -----------------
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253 Workflow position
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254 -----------------
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255
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256 **Upstream tools**
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257
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258 +-------------------------------+------------------------------+---------+
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259 | Name | output file |format |
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260 +===============================+==============================+=========+
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261 | Read.DataSet.Microarray | MicroArrayObject.RData | Rdat |
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262 +-------------------------------+------------------------------+---------+
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263
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264
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265 **Downstream tools**
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266
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267 +-----------------------------------------------+----------------------------------------------+---------+
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268 | Name | Output file | Format |
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269 +===============================================+==============================================+=========+
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270 |Tests and Selection | Test.results.tsv | Tabular |
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271 +-----------------------------------------------+----------------------------------------------+---------+
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272
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273 -----------
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274 Input files
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275 -----------
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276
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277 +---------------------------+------------+
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278 | Parameter : num + label | Format |
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279 +===========================+============+
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280 | Image | Rdata |
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281 +---------------------------+------------+
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282 | Methods parmeters | Numeric |
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283 +---------------------------+------------+
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284
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285 ------------
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286 Output files
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287 ------------
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288
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289 **Microarray.Preprocessing.RData**
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290
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291 **Matrix.Data.tsv**
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292
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293 ------------------------------
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294 General schema of the workflow
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295 ------------------------------
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296
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297 https://bensellak.github.io/microarrays-galaxy/workflow.png
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298
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299
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300 </help>
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301 <expand macro="R_citation">
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302 </expand>
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303 </tool>
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