--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selectionExtracted.xml	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,111 @@
+<tool id="markersSelection" name="Markers selection" force_history_refresh="True" version="0.1.0">
+  <description> of previously extracted signal</description>
+  <command>
+  	<![CDATA[ 
+        Rscript 
+        ${__tool_directory__}/selectionExtracted.R 
+    --input '$input' 
+  	--response '$response' 
+  	--new_file_path '$__new_file_path__' 
+  	--folds '$folds' 
+  	--loss '$loss' 
+  	--outputlog '$outputlog' 
+  	--output '$output' 
+  	--log '$log'
+  	]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
+	<param name="response" type="data" format="csv" label="Data response" help="Data response csv file. See below for more information on file format" />    
+	<param name="folds" type="integer" min="1" value="10" label ="Number of folds for cross validation" help="Integer between 1 and number of file in the .cel file dataset"/>
+    <param name="loss" type="select" multiple="false" label="Response type">
+      	<option value="linear">Linear</option>
+    	<option value="logistic">Logistic</option>
+    </param>
+   
+	<param name="outputgraph" type="select" label="Output figures">
+        <option value="TRUE">Yes</option>
+        <option value="FALSE">No</option>
+     </param>    
+    <param name="outputlog" type="select" label="Output log">
+        <option value="TRUE">Yes</option>
+        <option value="FALSE">No</option>
+    </param>    
+  </inputs>       
+  <outputs>
+    <data format="tabular" name="output" label="selection of ${input.name}" />
+    <data format="log" name="log" label="log of selection of ${input.name}" >
+    	<filter>outputlog == "TRUE"</filter>
+    </data>
+  </outputs>
+  <stdio>
+    <exit_code range="1:"   level="fatal"   description="See logs for more details" />
+   </stdio>
+  <help>
+  **What it does**
+   	    	
+This tool selects some relevant markers according to a response using penalized regressions.
+  
+Input:
+
+*A tabular text file containing 3 fixed columns and 1 column per sample:*
+	
+	- chr: Chromosome.
+	- position: Genomic position (in bp).
+  	- probeNames: Names of the probes.
+  	- One column per sample which contain the copy number signal for each sample.
+
+Output:
+  	
+*A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNP):*
+	
+	- chr: Chromosome containing the selected SNP.
+  	- position: Position of the selected SNP.
+	- index: Index of the selected SNP.
+	- names: Name of the selected SNP.
+	- coefficient: Regression coefficient of the selected SNP.
+
+-----
+
+**Data Response csv file**
+     	
+Data response csv file format:
+	
+	- The first column contains the names of the different files of the dataset.
+     	 
+	- The second column is the response associated with each file. 
+     	
+	- Column names of these two columns are respectively files and response.
+
+	- Columns are separated by a comma
+     	
+	- *Extensions of the files (.CEL for example) should be removed*
+
+
+     	
+**Example** 
+
+Let 3 .cel files in the studied dataset ::
+     	
+     	patient1.cel
+     	patient2.cel
+     	patient3.cel 
+     	
+The csv file should look like this ::
+     	
+     	files,response
+     	patient1,1.92145
+     	patient2,2.12481
+     	patient3,1.23545
+
+
+-----
+  	   	
+**Citation**
+	
+If you use this tool please cite : 
+
+`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint &lt;http://fr.arxiv.org/abs/1401.5035&gt;`_
+  
+ </help>
+</tool>