Mercurial > repos > proteomisc > preprocess_dataset
comparison preprocess_datasets/Preprocess_DataSet.xml @ 17:53793f67dd18 draft
Uploaded
| author | proteomisc |
|---|---|
| date | Sun, 03 Dec 2023 16:43:52 +0000 |
| parents | 0d544d449cca |
| children | c0cc4bdf07af |
comparison
equal
deleted
inserted
replaced
| 16:a73997df371a | 17:53793f67dd18 |
|---|---|
| 1 <tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="7"> | 1 <tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="11"> |
| 2 <description> Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization. </description> | 2 <description> Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization. </description> |
| 3 <macros> | 3 <macros> |
| 4 <import>citations.xml</import> | 4 <import>citations.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 26 <![CDATA[ | 26 <![CDATA[ |
| 27 Rscript | 27 Rscript |
| 28 #if $technologies.technology == "Affymetrix": | 28 #if $technologies.technology == "Affymetrix": |
| 29 '$__tool_directory__/Affymetrix_Preprocessing.R' | 29 '$__tool_directory__/Affymetrix_Preprocessing.R' |
| 30 thefunctions "AffymetrixPreprocessingFunction" | 30 thefunctions "AffymetrixPreprocessingFunction" |
| 31 path "pathtemp" | |
| 32 image $image | 31 image $image |
| 33 backgroundcorrection_method $technologies.BackgroundCorrectionA | 32 backgroundcorrection_method $technologies.BackgroundCorrectionA |
| 34 normalization_method $technologies.NormalizationA | 33 normalization_method $technologies.NormalizationA |
| 35 summary_method $technologies.SummarizationA | 34 summary_method $technologies.SummarizationA |
| 36 #elif $technologies.technology == "Agilent": | 35 #elif $technologies.technology == "Agilent": |
| 37 #if $technologies.channelsA.channelA == "one": | 36 #if $technologies.channelsA.channelA == "one": |
| 38 '$__tool_directory__/Agilent_One_Color_Preprocessing.R' | 37 '$__tool_directory__/Agilent_One_Color_Preprocessing.R' |
| 39 thefunction "AgilentOneColorPreprocessingFunction" | 38 thefunction "AgilentOneColorPreprocessingFunction" |
| 40 path "pathtemp" | |
| 41 image $image | 39 image $image |
| 42 methodBC $technologies.channelsA.BackgroundCorrectionAG | 40 methodBC $technologies.channelsA.BackgroundCorrectionAG |
| 43 methodNBA $technologies.channelsA.methodNBAAG | 41 methodNBA $technologies.channelsA.methodNBAAG |
| 44 #else: | 42 #else: |
| 45 '$__tool_directory__/Agilent_Two_Colors_Preprocessing.R' | 43 '$__tool_directory__/Agilent_Two_Colors_Preprocessing.R' |
| 46 thefunction "AgilentTwoChannelsPreprocessingFunction" | 44 thefunction "AgilentTwoChannelsPreprocessingFunction" |
| 47 path "pathtemp" | |
| 48 image $image | 45 image $image |
| 49 methodBC $technologies.channelsA.BackgroundCorrectionAGT | 46 methodBC $technologies.channelsA.BackgroundCorrectionAGT |
| 50 methodNWA $technologies.channelsA.methodNWAAGT | 47 methodNWA $technologies.channelsA.methodNWAAGT |
| 51 methodNBA $technologies.channelsA.methodNBAAGT | 48 methodNBA $technologies.channelsA.methodNBAAGT |
| 52 #end if | 49 #end if |
| 53 #else: | 50 #else: |
| 54 #if $technologies.channelsG.channelG == "one" | 51 #if $technologies.channelsG.channelG == "one" |
| 55 '$__tool_directory__/GenePix_One_Color_Preprocessing.R' | 52 '$__tool_directory__/GenePix_One_Color_Preprocessing.R' |
| 56 thefunction "GenePixOneColorPreprocessingFunction" | 53 thefunction "GenePixOneColorPreprocessingFunction" |
| 57 path "pathtemp" | |
| 58 image $image | 54 image $image |
| 59 methodBC $technologies.channelsG.BackgroundCorrectionG | 55 methodBC $technologies.channelsG.BackgroundCorrectionG |
| 60 methodNBA $technologies.channelsG.methodNBAG | 56 methodNBA $technologies.channelsG.methodNBAG |
| 61 #else: | 57 #else: |
| 62 '$__tool_directory__/GenePix_Two_Colors_Preprocessing.R' | 58 '$__tool_directory__/GenePix_Two_Colors_Preprocessing.R' |
| 63 thefunction "GenePixTwoChannelsPreprocessingFunction" | 59 thefunction "GenePixTwoChannelsPreprocessingFunction" |
| 64 path "pathtemp" | |
| 65 image $image | 60 image $image |
| 66 methodBC $technologies.channelsG.BackgroundCorrectionGT | 61 methodBC $technologies.channelsG.BackgroundCorrectionGT |
| 67 methodNWA $technologies.channelsG.methodNWAGT | 62 methodNWA $technologies.channelsG.methodNWAGT |
| 68 methodNBA $technologies.channelsG.methodNBAGT | 63 methodNBA $technologies.channelsG.methodNBAGT |
| 69 #end if | 64 #end if |