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diff preprocess_datasets/Preprocess_DataSet.xml @ 27:b5eac045873c draft

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author proteomisc
date Mon, 04 Dec 2023 12:41:06 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_datasets/Preprocess_DataSet.xml	Mon Dec 04 12:41:06 2023 +0000
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+<tool id="Preprocess_DataSet" name="Preprocess MicroArrays DataSets" version="15">
+    <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-biocmanager</requirement>
+		<requirement type="package">pandoc</requirement>
+        <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" 
+            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" 
+            	image $image 
+            	methodBC $technologies.channelsA.BackgroundCorrectionAG
+            	methodNBA $technologies.channelsA.methodNBAAG
+	    #else: 
+                '$__tool_directory__/Agilent_Two_Colors_Preprocessing.R' 
+                thefunction "AgilentTwoChannelsPreprocessingFunction" 
+                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" 
+            	image $image 
+            	methodBC $technologies.channelsG.BackgroundCorrectionG  
+            	methodNBA $technologies.channelsG.methodNBAG
+	    #else:
+                '$__tool_directory__/GenePix_Two_Colors_Preprocessing.R' 
+                thefunction "GenePixTwoChannelsPreprocessingFunction" 
+                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>