--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractCN.xml	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,222 @@
+<tool id="extract" name="Extract" force_history_refresh="True" version="1.1.0">
+  <description>copy number or allele B fraction signal</description>
+  <requirement type="package" version="1.1.2">mpagenomics</requirement>
+   <command>
+    	<![CDATA[ 
+        Rscript 
+        ${__tool_directory__}/extractCN.R	
+    --chrom '$chrom'
+  	--input '$input'
+  	--output '$output' 
+  	--new_file_path '$__new_file_path__'
+  	#if $settings.settingsType == "file":
+  		--settings_type '$settings.inputs'
+  	#end if
+  	#if $settings.settingsType == "dataset":
+  		--settings_type 'dataset'
+  	#end if
+  	#if $settingsSNP.signal == "fracB":
+  		--settings_snp 'TRUE'
+  		
+  		#if $settingsSNP.sym.symmetrize=="TRUE"
+  			--settings_tumor '$tumorcsvFracBsym'
+  		#elif $settingsSNP.sym.symmetrize=="FALSE"
+  			#if $settingsSNP.sym.settingsTumorFracB.settingsTypeTumorFracB == "standard":
+  				--settings_tumor 'None'
+  			#elif  $settingsSNP.sym.settingsTumorFracB.settingsTypeTumorFracB == "tumor":
+  				--settings_tumor '$tumorcsvFracB'
+   			#end if
+  		#end if
+  		--symmetrize '$settingsSNP.sym.symmetrize'
+  	#else
+  		--settings_snp '$settingsSNP.snp'
+  		#if $settingsSNP.settingsTumor.settingsTypeTumor == "standard":
+  			--settings_tumor 'None'
+  		#elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor":
+  			--settings_tumor '$tumorcsvCN'
+  		#end if
+  	#end if
+  	--outputlog '$outputlog'
+  	--log '$log' 
+  	--settings_signal '$settingsSNP.signal'
+  	--userid '$__user_id__'
+        	]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
+	<conditional name="settings">
+      <param name="settingsType" type="select" label="Files selection Mode" help="Select the whole cel files dataset or pick-up only few files from the dataset">
+        <option value="dataset">Select whole dataset</option>
+        <option value="file">Select file individually</option>
+      </param>
+      <when value="dataset"/>
+      <when value="file">
+        <param name="inputs" type="select" format="cel" multiple="true" label="Cel files">
+        <options from_dataset="input">
+    		<column name="name" index="0"/>
+    		<column name="value" index="0"/>
+		</options>
+		</param>
+	   </when>
+    </conditional>
+    
+    <conditional name="settingsSNP">
+    	<param name="signal" type="select" multiple="false" label="Signal you want to work on">
+     		<option value="CN">CN</option>
+      		<option value="fracB">fracB</option>
+    	</param> 
+    	<when value="fracB">
+    		<conditional name="sym">
+    			<param name="symmetrize" type="select" label="Symmetrize allele B signal">
+        			<option value="TRUE">Yes</option>
+        			<option value="FALSE">No</option>
+    			</param>
+    			<when value="TRUE">
+    				<param name="tumorcsvFracBsym" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/>
+    			</when>
+    			<when value="FALSE">
+    				<conditional name="settingsTumorFracB">
+      					<param name="settingsTypeTumorFracB" type="select" label="Reference">
+        					<option value="standard">Study without reference</option>
+        					<option value="tumor">Normal-tumor study</option>
+      					</param>
+      					<when value="standard"/>
+      					<when value="tumor">
+        					<param name="tumorcsvFracB" type="data" format="csv" label="Tumor boost csv file" help="Normal-tumor csv file. See below for more information."/>
+      					</when>
+    				</conditional>        	
+    			</when>
+    		</conditional>
+    	</when>
+		<when value="CN">
+			<conditional name="settingsTumor">
+      			<param name="settingsTypeTumor" type="select" label="Reference">
+        			<option value="standard">Study without reference</option>
+        			<option value="tumor">Normal-tumor study</option>
+      			</param>
+      			<when value="standard"/>
+      			<when value="tumor">
+        			<param name="tumorcsvCN" type="data" format="csv" label="Normal tumor csv file" help="Normal-tumor csv file. See below for more information."/>
+      			</when>
+    		</conditional>        	
+     		<param name="snp" type="select" label="Select Probes">
+        		<option value="FALSE">CN and SNP probes</option>
+        		<option value="TRUE">Only SNP probes</option>
+    		</param>
+    	</when>
+    </conditional>
+         
+    <!--param name="chrom" type="text" value="All" label="Chromosomes" help="Chromosomes to segment. Use comma to choose multiple chromosomes: e.g. 1, 3, 8. Use 'All' for a segmentation on all chromosomes" /-->
+    
+    <param  name="chrom" type="select" size="6" multiple="true" label="Chromosomes" help="You can select several chromosomeleave blank for all chromosomes">
+      <option value="All">All</option>
+      <option value="1">chr 1</option>
+      <option value="2">chr 2</option>
+      <option value="3">chr 3</option>
+      <option value="4">chr 4</option>
+      <option value="5">chr 5</option>
+      <option value="6">chr 6</option>
+      <option value="7">chr 7</option>
+      <option value="8">chr 8</option>
+      <option value="9">chr 9</option>
+      <option value="10">chr 10</option>
+      <option value="11">chr 11</option>
+      <option value="12">chr 12</option>
+      <option value="13">chr 13</option>
+      <option value="14">chr 14</option>
+      <option value="15">chr 15</option>
+      <option value="16">chr 16</option>
+      <option value="17">chr 17</option>
+      <option value="18">chr 18</option>
+      <option value="19">chr 19</option>
+      <option value="20">chr 20</option>
+      <option value="21">chr 21</option>
+      <option value="22">chr 22</option>
+      <option value="23">chr 23</option>
+      <option value="24">chr 24</option>
+      <option value="25">chr 25</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="sef" name="output" label="signal extraction of ${input.name}" />
+    <data format="log" name="log" label="log of signal extraction of ${input.name}">
+    	<filter>outputlog == "TRUE"</filter>
+    </data>
+   </outputs>
+   <stdio>
+    <exit_code range="1:"   level="fatal"   description="See logs for more details" />
+   </stdio>
+<help>
+.. class:: warningmark
+
+Data normalization must be run (with the data normalization tool) prior to signal extraction.
+
+-----
+
+**What it does**     	
+This tool extracts the copy number profile from the normalized data. 
+	
+Outputs:
+  	
+*A tabular text file containing 3 fixed columns and 1 column per sample:*
+	
+	- chr: Chromosome.
+	- position: Genomic position (in bp).
+	- probeNames: Name of the probes of the microarray.
+	- One column per sample which contains the copy number profile for each sample.
+  		
+-----
+  		
+**Normal-tumor study**
+     	
+In cases where normal (control) samples match to tumor samples, normalization can be improved using TumorBoost. In this case, a normal-tumor csv file must be provided :
+
+	- The first column contains the names of the files corresponding to normal samples of the dataset.
+     	 
+	- The second column contains the names of the tumor samples files. 
+     	
+	- Column names of these two columns are respectively normal and tumor.
+     	
+	- Columns are separated by a comma.
+     	
+	- *Extensions of the files (.CEL for example) should be removed*
+
+
+     	
+**Example** 
+
+Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) ::
+     	
+     	patient1_normal.cel
+     	patient1_tumor.cel
+     	patient2_normal.cel
+     	patient2_tumor.cel
+     	patient3_normal.cel 
+     	patient3_tumor.cel
+      	
+
+The csv file should look like this ::
+     	
+     	normal,tumor
+     	patient1_normal,patient1_tumor
+     	patient2_normal,patient2_tumor
+     	patient3_normal,patient3_tumor
+
+-----     	  		
+
+     	
+**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>