--- a/extractCN.xml	Tue Jun 16 04:34:09 2020 -0400
+++ b/extractCN.xml	Mon Apr 12 14:47:09 2021 +0000
@@ -1,14 +1,17 @@
-<tool id="extract" name="Extract" force_history_refresh="True" version="1.1.0">
+<tool id="extract" name="Extract" version="1.2.0">
   <description>copy number or allele B fraction signal</description>
-  <requirement type="package" version="1.1.2">mpagenomics</requirement>
-   <command>
+   <requirements>
+        <container type="docker">sblanck/mpagenomicsdependencies</container>
+  </requirements>
+  <command>
     	<![CDATA[ 
         Rscript 
         ${__tool_directory__}/extractCN.R	
     --chrom '$chrom'
   	--input '$input'
+  	--zip '$zip'
   	--output '$output' 
-  	--new_file_path '$__new_file_path__'
+  	--new_file_path '$output.extra_files_path'
   	#if $settings.settingsType == "file":
   		--settings_type '$settings.inputs'
   	#end if
@@ -17,23 +20,14 @@
   	#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 '$settingsSNP.sym.symmetrize'
+  		--settings_tumor '$settingsSNP.tumorcsvFracBsym'
+  		--symmetrize 'TRUE'
   	#else
   		--settings_snp '$settingsSNP.snp'
   		#if $settingsSNP.settingsTumor.settingsTypeTumor == "standard":
   			--settings_tumor 'None'
   		#elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor":
-  			--settings_tumor '$tumorcsvCN'
+		--settings_tumor '${settingsSNP.settingsTumor.tumorcsvCN}'
   		#end if
   	#end if
   	--outputlog '$outputlog'
@@ -44,6 +38,7 @@
   </command>
   <inputs>
     <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
+	  <param name="zip" type="data" format="zip" label="Zip results file" help="Zip results 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>
@@ -66,14 +61,14 @@
       		<option value="fracB">fracB</option>
     	</param> 
     	<when value="fracB">
-    		<conditional name="sym">
+    		<!--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">
+    			<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>
     			<when value="FALSE">
     				<conditional name="settingsTumorFracB">
       					<param name="settingsTypeTumorFracB" type="select" label="Reference">
@@ -85,8 +80,8 @@
         					<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-->
+    		<!--/conditional-->
     	</when>
 		<when value="CN">
 			<conditional name="settingsTumor">
@@ -109,7 +104,6 @@
     <!--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>
@@ -144,8 +138,8 @@
     </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}">
+	  <data format="sef" name="output" label="signal extraction of ${settingsSNP.signal} of ${input.name}" />
+    <data format="log" name="log" label="log of signal extraction of ${settingsSNP.signal} of ${input.name}">
     	<filter>outputlog == "TRUE"</filter>
     </data>
    </outputs>