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changeset 7:cc619066d6f7 draft

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author proteomisc
date Sat, 02 Dec 2023 15:48:52 +0000
parents ee7df29f66cd
children dcfc14781d54
files Preprocess_DataSet.xml preprocess_datasets/Preprocess_DataSet.xml
diffstat 2 files changed, 0 insertions(+), 612 deletions(-) [+]
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--- a/Preprocess_DataSet.xml	Sat Dec 02 15:48:01 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,306 +0,0 @@
-<tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="3.11">
-    <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>
-    </macros>  
-    <requirements>
-        <requirement type="package">r-base</requirement>
-        <requirement type="package">r-batch</requirement>
-        <requirement type="package">bioconductor-affyplm</requirement>
-        <requirement type="package">bioconductor-affy</requirement>
-        <requirement type="package">bioconductor-annotate</requirement>
-        <requirement type="package">r-knitr</requirement>
-        <requirement type="package">bioconductor-marray</requirement>
-        <requirement type="package">r-idpmisc</requirement>
-        <requirement type="package">r-kernsmooth</requirement>
-        <requirement type="package">r-rmarkdown</requirement>
-        <requirement type="package">r-markdown</requirement>
-        <requirement type="package">bioconductor-limma</requirement>
-        <requirement type="package">r-idpmisc</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>   
-    <command>
-    <![CDATA[
-    Rscript
-        #if $technologies.technology == "Affymetrix":
-            '$__tool_directory__/Affymetrix_Preprocessing.R' 
-            thefunctions "AffymetrixPreprocessingFunction" 
-            path "pathtemp" 
-            image $image 
-            backgroundcorrection_method $technologies.BackgroundCorrectionA 
-            normalization_method $technologies.NormalizationA
-            summary_method $technologies.SummarizationA
-        #elif $technologies.technology == "Agilent":
-	    #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 
-                methodNBA $technologies.channelsA.methodNBAAGT 
-            #end if 
-        #else:
-            #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
-                methodNBA $technologies.channelsG.methodNBAGT 
-            #end if 
-        #end if
-        w $w
-        h $h
-    ]]>
-    </command> 
-    <inputs>
-        <param name="image" type="data" format="rdata" label="Project microarray as a binary rdata" help="Last output from tool read dataset." >
-            <validator type="expression" message="Please select output dataset from read dataset tool ">'Read.Project'  in value.name</validator>
-        </param>
-        <conditional name="technologies">
-            <param name="technology" type="select" label="Select the technology">
-                <option value="Affymetrix" selected="true">Affymetrix</option>
-          	<option value="Agilent">Agilent</option>
-          	<option value="GenePix">GenePix</option>
-            </param>
-            <when value="Affymetrix">
-                <param name="BackgroundCorrectionA" type="select" label="Background correction method.">
-          	    <option value="mas" selected="true">Mas</option>
-                    <option value="rma">Rma</option>
-          	    <option value="none">None</option>
-    	        </param>
-                <param name="NormalizationA" type="select" label="Normalization method.">
-          	    <option value="quantiles" selected="true">Quantiles</option>
-                    <option value="quantiles.robust">Quantiles robust</option>
-		    <option value="quantiles.probeset">Quantiles Probeset</option>
-                    <option value="constant">Constant</option>
-          	    <option value="contrasts">Contrasts</option>
-                    <option value="invariantset">Invariantset</option>
-                    <option value="loess">Loess</option>
-          	    <option value="qspline">QSPline</option>
-                    <option value="scaling">Scaling</option>
-		    <option value="vsn">VSN</option>
-    	       </param> 
-               <param name="SummarizationA" type="select" label="Summarization method.">
-          	    <option value="median.polish" selected="true">Median.polish</option>
-                    <option value="tukey.biweight">Tukey.biweight</option>
-                    <option value="average.log">Average.log</option>
-          	    <option value="log.average">Log.average</option>
-                    <option value="rlm">Rlm</option>
-                    <option value="lm">Lm</option>
-                    <option value="log.median">Log.median</option>
-                    <option value="median.log">Median.log</option>
-          	    <option value="log.2nd.largest">Log.2nd.largest</option>
-               </param> 
-            </when>
-            <when value="Agilent">
-                <conditional name="channelsA">
-            	    <param name="channelA" type="select" label="Select the number of channels">
-                        <option value="one" selected="true">One</option>
-          	        <option value="two">Two</option>
-            	    </param>
-                <when value="one">
-               	    <param name="BackgroundCorrectionAG" type="select" label="Background correction method.">
-          	        <option value="auto" selected="true">Auto</option>
-                    	<option value="none">None</option>
-          	    	<option value="subtract">Subtract</option>
-		    	<option value="half">Half</option>
-                    	<option value="minimum">Minimum</option>
-          	    	<option value="movingmin">MovingMin</option>
-		    	<option value="edwards">Edwards</option>
-          	    	<option value="normexp">NormExp</option>
-    	       	    </param>
-               	    <param name="methodNBAAG" type="select" label="Normalization between arrays.">
-          	        <option value="scale" selected="true">Scale</option>
-                    	<option value="quantile">Quantile</option>
-                    	<option value="cyclicloess">CyclicLoess</option>
-    	       	    </param> 
-            	</when>
-            	<when value="two">
-               	    <param name="BackgroundCorrectionAGT" type="select" label="Background correction method.">
-          	        <option value="auto" selected="true">Auto</option>
-                    	<option value="none">None</option>
-          	    	<option value="subtract">Subtract</option>
-		    	<option value="half">Half</option>
-                    	<option value="minimum">Minimum</option>
-          	    	<option value="movingmin">MovingMin</option>
-		    	<option value="edwards">Edwards</option>
-          	    	<option value="normexp">NormExp</option>
-    	            </param>
-               	    <param name="methodNWAAGT" type="select" label="Normalization within arrays.">
-          	        <option value="median" selected="true">Median</option>
-                    	<option value="loess">Loess</option>
-                    	<option value="printtiploess">PrintTiploess</option>  
-    	       	    </param> 
-               	    <param name="methodNBAAGT" type="select" label="Normalization between arrays.">
-          	        <option value="scale" selected="true">Scale</option>
-                    	<option value="quantile">Quantile</option>
-                    	<option value="Aquantile">AQuantile</option>  
-                    	<option value="cyclicloess">CyclicLoess</option>
-    	       	    </param> 
-            	</when>
-                </conditional>
-            </when>
-            <when value="GenePix">
-                <conditional name="channelsG">
-            	    <param name="channelG" type="select" label="Select the number of channels">
-                        <option value="one" selected="true">One</option>
-          		<option value="two">Two</option>
-            	    </param>
-            	    <when value="one">
-               	        <param name="BackgroundCorrectionG" type="select" label="Background correction method.">
-          	    	    <option value="auto" selected="true">Auto</option>
-                    	    <option value="none">None</option>
-          	    	    <option value="subtract">Subtract</option>
-		    	    <option value="half">Half</option>
-                    	    <option value="minimum">Minimum</option>
-          	    	    <option value="movingmin">MovingMin</option>
-		    	    <option value="edwards">Edwards</option>
-          	    	    <option value="normexp">NormExp</option>
-    	       		</param>
-               		<param name="methodNBAG" type="select" label="Normalization between arrays.">
-          	    		<!--<option value="scale" selected="true">Scale</option>-->
-                    		<option value="quantile" selected="true">Quantile</option>
-                                 <option value="scale">Scale</option>
-                    		<option value="cyclicloess">CyclicLoess</option>
-    	       		</param> 
-            	    </when>
-            	    <when value="two">
-               	        <param name="BackgroundCorrectionGT" type="select" label="Background correction method.">
-          	    	    <option value="auto" selected="true">Auto</option>
-                    	    <option value="none">None</option>
-          	    	    <option value="subtract">Subtract</option>
-		    	    <option value="half">Half</option>
-                    	    <option value="minimum">Minimum</option>
-          	    	    <option value="movingmin">MovingMin</option>
-		            <option value="edwards">Edwards</option>
-          	    	    <option value="normexp">NormExp</option>
-    	       		</param>
-               		<param name="methodNWAGT" type="select" label="Normalization within arrays.">
-          	    	    <option value="median" selected="true">Median</option>
-                    	    <option value="loess">Loess</option>
-                    	    <option value="printtiploess">PrintTiploess</option>  
-    	       		</param> 
-               		<param name="methodNBAGT" type="select" label="Normalization between arrays.">
-          	    		<!--<option value="scale" >Scale</option>-->
-                    	    <option value="quantile" selected="true">Quantile</option>
-                            <option value="scale">Scale</option>
-                            <option value="cyclicloess">CyclicLoess</option>
-                    	    <option value="Aquantile">AQuantile</option>  
-    	       		</param> 
-            	    </when>
-                </conditional>
-            </when>
-        </conditional>
-        <param name="w" type="integer" value="1024" label="Plot's width" />
-        <param name="h" type="integer" value="1024" label="Plot's height" />
-    </inputs>
-    <outputs>
-        <data name="ProcessDataSetRData" format="rdata" from_work_dir="MicroArray.Preprocessing.RData" label="Preprocess.Project.Data.RData" />
-        <data name="Matrix.Data" format="tabular" from_work_dir="Matrix.Data.tsv" label="Matrix.Data.tsv" />
-        <data name="Preprocessing.Plots" format="html" from_work_dir="PreprocessingPlots.html" label="Preprocessing.Plots.html" />   
-    </outputs>
-     <tests>
-        <test>
-            <param name="image" ftype="rdata" value="Read.Project.Data.RData" />  
-            <param name="technologies|technology" value="GenePix"/>
-            <param name="technologies|channelsG|channelG" value="two"/>
-            <param name="technologies|channelsG|BackgroundCorrectionGT" value="auto"/>
-            <param name="technologies|channelsG|methodNWAGT" value="median"/>
-            <param name="technologies|channelsG|methodNBAGT" value="quantile"/>
-            <output name="ProcessDataSetRData"  ftype="rdata" file="Preprocess.Project.Data.RData" compare="sim_size" >
-            </output>
-            <output name="Matrix.Data"  ftype="tabular" file="Matrix.Data.tsv" >
-            </output>
-            <output name="Preprocessing.Plots"  ftype="html" file="Preprocessing.Plots.html" compare="sim_size">
-            </output>
-        </test>
-    </tests>
-    <help>
-		
-.. class:: infomark
-
-**Authors**  T.Bensellak, B.Ettetuani.
-
----------------------------------------------------
-
-==================================
-Preprocessing Microarray DataSet
-==================================
-
------------
-Description
------------
-
-This tool is used as first phase of the global workflow, the preprocessing .
-
------------------
-Workflow position
------------------
-
-**Upstream tools**
-
-+-------------------------------+------------------------------+---------+
-| Name                          | output file                  |format   |
-+===============================+==============================+=========+
-| Read.DataSet.Microarray       |  MicroArrayObject.RData      | Rdat    |			
-+-------------------------------+------------------------------+---------+
-
-
-**Downstream tools**
-
-+-----------------------------------------------+----------------------------------------------+---------+
-| Name                                          | Output file                                  | Format  |
-+===============================================+==============================================+=========+
-|Tests and Selection                            | Test.results.tsv                             | Tabular |
-+-----------------------------------------------+----------------------------------------------+---------+
-
------------
-Input files
------------
-
-+---------------------------+------------+
-| Parameter : num + label   |   Format   |
-+===========================+============+
-| Image                     |   Rdata    |
-+---------------------------+------------+
-| Methods parmeters         |   Numeric  |
-+---------------------------+------------+
-
-------------
-Output files
-------------
-
-**Microarray.Preprocessing.RData**
-
-**Matrix.Data.tsv**
-
-------------------------------
-General schema of the workflow
-------------------------------
-
-https://bensellak.github.io/microarrays-galaxy/workflow.png
-
-
-   </help>
-   <expand macro="R_citation">
-   </expand>
-</tool>
--- a/preprocess_datasets/Preprocess_DataSet.xml	Sat Dec 02 15:48:01 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,306 +0,0 @@
-<tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="3.11">
-    <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>
-    </macros>  
-    <requirements>
-        <requirement type="package">r-base</requirement>
-        <requirement type="package">r-batch</requirement>
-        <requirement type="package">bioconductor-affyplm</requirement>
-        <requirement type="package">bioconductor-affy</requirement>
-        <requirement type="package">bioconductor-annotate</requirement>
-        <requirement type="package">r-knitr</requirement>
-        <requirement type="package">bioconductor-marray</requirement>
-        <requirement type="package">r-idpmisc</requirement>
-        <requirement type="package">r-kernsmooth</requirement>
-        <requirement type="package">r-rmarkdown</requirement>
-        <requirement type="package">r-markdown</requirement>
-        <requirement type="package">bioconductor-limma</requirement>
-        <requirement type="package">r-idpmisc</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>   
-    <command>
-    <![CDATA[
-    Rscript
-        #if $technologies.technology == "Affymetrix":
-            '$__tool_directory__/Affymetrix_Preprocessing.R' 
-            thefunctions "AffymetrixPreprocessingFunction" 
-            path "pathtemp" 
-            image $image 
-            backgroundcorrection_method $technologies.BackgroundCorrectionA 
-            normalization_method $technologies.NormalizationA
-            summary_method $technologies.SummarizationA
-        #elif $technologies.technology == "Agilent":
-	    #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 
-                methodNBA $technologies.channelsA.methodNBAAGT 
-            #end if 
-        #else:
-            #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
-                methodNBA $technologies.channelsG.methodNBAGT 
-            #end if 
-        #end if
-        w $w
-        h $h
-    ]]>
-    </command> 
-    <inputs>
-        <param name="image" type="data" format="rdata" label="Project microarray as a binary rdata" help="Last output from tool read dataset." >
-            <validator type="expression" message="Please select output dataset from read dataset tool ">'Read.Project'  in value.name</validator>
-        </param>
-        <conditional name="technologies">
-            <param name="technology" type="select" label="Select the technology">
-                <option value="Affymetrix" selected="true">Affymetrix</option>
-          	<option value="Agilent">Agilent</option>
-          	<option value="GenePix">GenePix</option>
-            </param>
-            <when value="Affymetrix">
-                <param name="BackgroundCorrectionA" type="select" label="Background correction method.">
-          	    <option value="mas" selected="true">Mas</option>
-                    <option value="rma">Rma</option>
-          	    <option value="none">None</option>
-    	        </param>
-                <param name="NormalizationA" type="select" label="Normalization method.">
-          	    <option value="quantiles" selected="true">Quantiles</option>
-                    <option value="quantiles.robust">Quantiles robust</option>
-		    <option value="quantiles.probeset">Quantiles Probeset</option>
-                    <option value="constant">Constant</option>
-          	    <option value="contrasts">Contrasts</option>
-                    <option value="invariantset">Invariantset</option>
-                    <option value="loess">Loess</option>
-          	    <option value="qspline">QSPline</option>
-                    <option value="scaling">Scaling</option>
-		    <option value="vsn">VSN</option>
-    	       </param> 
-               <param name="SummarizationA" type="select" label="Summarization method.">
-          	    <option value="median.polish" selected="true">Median.polish</option>
-                    <option value="tukey.biweight">Tukey.biweight</option>
-                    <option value="average.log">Average.log</option>
-          	    <option value="log.average">Log.average</option>
-                    <option value="rlm">Rlm</option>
-                    <option value="lm">Lm</option>
-                    <option value="log.median">Log.median</option>
-                    <option value="median.log">Median.log</option>
-          	    <option value="log.2nd.largest">Log.2nd.largest</option>
-               </param> 
-            </when>
-            <when value="Agilent">
-                <conditional name="channelsA">
-            	    <param name="channelA" type="select" label="Select the number of channels">
-                        <option value="one" selected="true">One</option>
-          	        <option value="two">Two</option>
-            	    </param>
-                <when value="one">
-               	    <param name="BackgroundCorrectionAG" type="select" label="Background correction method.">
-          	        <option value="auto" selected="true">Auto</option>
-                    	<option value="none">None</option>
-          	    	<option value="subtract">Subtract</option>
-		    	<option value="half">Half</option>
-                    	<option value="minimum">Minimum</option>
-          	    	<option value="movingmin">MovingMin</option>
-		    	<option value="edwards">Edwards</option>
-          	    	<option value="normexp">NormExp</option>
-    	       	    </param>
-               	    <param name="methodNBAAG" type="select" label="Normalization between arrays.">
-          	        <option value="scale" selected="true">Scale</option>
-                    	<option value="quantile">Quantile</option>
-                    	<option value="cyclicloess">CyclicLoess</option>
-    	       	    </param> 
-            	</when>
-            	<when value="two">
-               	    <param name="BackgroundCorrectionAGT" type="select" label="Background correction method.">
-          	        <option value="auto" selected="true">Auto</option>
-                    	<option value="none">None</option>
-          	    	<option value="subtract">Subtract</option>
-		    	<option value="half">Half</option>
-                    	<option value="minimum">Minimum</option>
-          	    	<option value="movingmin">MovingMin</option>
-		    	<option value="edwards">Edwards</option>
-          	    	<option value="normexp">NormExp</option>
-    	            </param>
-               	    <param name="methodNWAAGT" type="select" label="Normalization within arrays.">
-          	        <option value="median" selected="true">Median</option>
-                    	<option value="loess">Loess</option>
-                    	<option value="printtiploess">PrintTiploess</option>  
-    	       	    </param> 
-               	    <param name="methodNBAAGT" type="select" label="Normalization between arrays.">
-          	        <option value="scale" selected="true">Scale</option>
-                    	<option value="quantile">Quantile</option>
-                    	<option value="Aquantile">AQuantile</option>  
-                    	<option value="cyclicloess">CyclicLoess</option>
-    	       	    </param> 
-            	</when>
-                </conditional>
-            </when>
-            <when value="GenePix">
-                <conditional name="channelsG">
-            	    <param name="channelG" type="select" label="Select the number of channels">
-                        <option value="one" selected="true">One</option>
-          		<option value="two">Two</option>
-            	    </param>
-            	    <when value="one">
-               	        <param name="BackgroundCorrectionG" type="select" label="Background correction method.">
-          	    	    <option value="auto" selected="true">Auto</option>
-                    	    <option value="none">None</option>
-          	    	    <option value="subtract">Subtract</option>
-		    	    <option value="half">Half</option>
-                    	    <option value="minimum">Minimum</option>
-          	    	    <option value="movingmin">MovingMin</option>
-		    	    <option value="edwards">Edwards</option>
-          	    	    <option value="normexp">NormExp</option>
-    	       		</param>
-               		<param name="methodNBAG" type="select" label="Normalization between arrays.">
-          	    		<!--<option value="scale" selected="true">Scale</option>-->
-                    		<option value="quantile" selected="true">Quantile</option>
-                                 <option value="scale">Scale</option>
-                    		<option value="cyclicloess">CyclicLoess</option>
-    	       		</param> 
-            	    </when>
-            	    <when value="two">
-               	        <param name="BackgroundCorrectionGT" type="select" label="Background correction method.">
-          	    	    <option value="auto" selected="true">Auto</option>
-                    	    <option value="none">None</option>
-          	    	    <option value="subtract">Subtract</option>
-		    	    <option value="half">Half</option>
-                    	    <option value="minimum">Minimum</option>
-          	    	    <option value="movingmin">MovingMin</option>
-		            <option value="edwards">Edwards</option>
-          	    	    <option value="normexp">NormExp</option>
-    	       		</param>
-               		<param name="methodNWAGT" type="select" label="Normalization within arrays.">
-          	    	    <option value="median" selected="true">Median</option>
-                    	    <option value="loess">Loess</option>
-                    	    <option value="printtiploess">PrintTiploess</option>  
-    	       		</param> 
-               		<param name="methodNBAGT" type="select" label="Normalization between arrays.">
-          	    		<!--<option value="scale" >Scale</option>-->
-                    	    <option value="quantile" selected="true">Quantile</option>
-                            <option value="scale">Scale</option>
-                            <option value="cyclicloess">CyclicLoess</option>
-                    	    <option value="Aquantile">AQuantile</option>  
-    	       		</param> 
-            	    </when>
-                </conditional>
-            </when>
-        </conditional>
-        <param name="w" type="integer" value="1024" label="Plot's width" />
-        <param name="h" type="integer" value="1024" label="Plot's height" />
-    </inputs>
-    <outputs>
-        <data name="ProcessDataSetRData" format="rdata" from_work_dir="MicroArray.Preprocessing.RData" label="Preprocess.Project.Data.RData" />
-        <data name="Matrix.Data" format="tabular" from_work_dir="Matrix.Data.tsv" label="Matrix.Data.tsv" />
-        <data name="Preprocessing.Plots" format="html" from_work_dir="PreprocessingPlots.html" label="Preprocessing.Plots.html" />   
-    </outputs>
-     <tests>
-        <test>
-            <param name="image" ftype="rdata" value="Read.Project.Data.RData" />  
-            <param name="technologies|technology" value="GenePix"/>
-            <param name="technologies|channelsG|channelG" value="two"/>
-            <param name="technologies|channelsG|BackgroundCorrectionGT" value="auto"/>
-            <param name="technologies|channelsG|methodNWAGT" value="median"/>
-            <param name="technologies|channelsG|methodNBAGT" value="quantile"/>
-            <output name="ProcessDataSetRData"  ftype="rdata" file="Preprocess.Project.Data.RData" compare="sim_size" >
-            </output>
-            <output name="Matrix.Data"  ftype="tabular" file="Matrix.Data.tsv" >
-            </output>
-            <output name="Preprocessing.Plots"  ftype="html" file="Preprocessing.Plots.html" compare="sim_size">
-            </output>
-        </test>
-    </tests>
-    <help>
-		
-.. class:: infomark
-
-**Authors**  T.Bensellak, B.Ettetuani.
-
----------------------------------------------------
-
-==================================
-Preprocessing Microarray DataSet
-==================================
-
------------
-Description
------------
-
-This tool is used as first phase of the global workflow, the preprocessing .
-
------------------
-Workflow position
------------------
-
-**Upstream tools**
-
-+-------------------------------+------------------------------+---------+
-| Name                          | output file                  |format   |
-+===============================+==============================+=========+
-| Read.DataSet.Microarray       |  MicroArrayObject.RData      | Rdat    |			
-+-------------------------------+------------------------------+---------+
-
-
-**Downstream tools**
-
-+-----------------------------------------------+----------------------------------------------+---------+
-| Name                                          | Output file                                  | Format  |
-+===============================================+==============================================+=========+
-|Tests and Selection                            | Test.results.tsv                             | Tabular |
-+-----------------------------------------------+----------------------------------------------+---------+
-
------------
-Input files
------------
-
-+---------------------------+------------+
-| Parameter : num + label   |   Format   |
-+===========================+============+
-| Image                     |   Rdata    |
-+---------------------------+------------+
-| Methods parmeters         |   Numeric  |
-+---------------------------+------------+
-
-------------
-Output files
-------------
-
-**Microarray.Preprocessing.RData**
-
-**Matrix.Data.tsv**
-
-------------------------------
-General schema of the workflow
-------------------------------
-
-https://bensellak.github.io/microarrays-galaxy/workflow.png
-
-
-   </help>
-   <expand macro="R_citation">
-   </expand>
-</tool>