# HG changeset patch
# User proteomisc
# Date 1701621832 0
# Node ID 53793f67dd18c3715a05245cecbfa03c37da7b75
# Parent  a73997df371a126a31972d9428a93e52e5b9c182
Uploaded

diff -r a73997df371a -r 53793f67dd18 preprocess_datasets/Preprocess_DataSet.xml
--- a/preprocess_datasets/Preprocess_DataSet.xml	Sun Dec 03 16:14:33 2023 +0000
+++ b/preprocess_datasets/Preprocess_DataSet.xml	Sun Dec 03 16:43:52 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="7">
+<tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="11">
     <description> Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization. </description>  
     <macros>
         <import>citations.xml</import>
@@ -28,7 +28,6 @@
         #if $technologies.technology == "Affymetrix":
             '$__tool_directory__/Affymetrix_Preprocessing.R' 
             thefunctions "AffymetrixPreprocessingFunction" 
-            path "pathtemp" 
             image $image 
             backgroundcorrection_method $technologies.BackgroundCorrectionA 
             normalization_method $technologies.NormalizationA
@@ -37,14 +36,12 @@
 	    #if $technologies.channelsA.channelA == "one":
             	'$__tool_directory__/Agilent_One_Color_Preprocessing.R'       
 	    	thefunction "AgilentOneColorPreprocessingFunction" 
-            	path "pathtemp" 
             	image $image 
             	methodBC $technologies.channelsA.BackgroundCorrectionAG
             	methodNBA $technologies.channelsA.methodNBAAG
 	    #else: 
                 '$__tool_directory__/Agilent_Two_Colors_Preprocessing.R' 
                 thefunction "AgilentTwoChannelsPreprocessingFunction" 
-                path "pathtemp" 
                 image $image 
                 methodBC $technologies.channelsA.BackgroundCorrectionAGT 
                 methodNWA $technologies.channelsA.methodNWAAGT 
@@ -54,14 +51,12 @@
             #if $technologies.channelsG.channelG == "one"
                 '$__tool_directory__/GenePix_One_Color_Preprocessing.R' 
 	    	thefunction "GenePixOneColorPreprocessingFunction" 
-            	path "pathtemp" 
             	image $image 
             	methodBC $technologies.channelsG.BackgroundCorrectionG  
             	methodNBA $technologies.channelsG.methodNBAG
 	    #else:
                 '$__tool_directory__/GenePix_Two_Colors_Preprocessing.R' 
                 thefunction "GenePixTwoChannelsPreprocessingFunction" 
-                path "pathtemp" 
                 image $image 
                 methodBC $technologies.channelsG.BackgroundCorrectionGT 
                 methodNWA $technologies.channelsG.methodNWAGT