--- a/segmentation.xml	Mon Apr 12 14:47:09 2021 +0000
+++ b/segmentation.xml	Tue Apr 20 13:11:24 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="segmentation" name="Segmentation and calling" version="1.2.0">
+<tool id="segmentation" name="Segmentation and calling" version="1.3.0">
   <description>of a previously normalized signal</description>
    <requirements>
         <container type="docker">sblanck/mpagenomicsdependencies</container>
@@ -7,42 +7,39 @@
     <![CDATA[ 
         Rscript 
         ${__tool_directory__}/segmentation.R 
-  		#if $signalType.signal == "CN":
-  			--nbcall '$signalType.nbcall' 
-  			--cellularity '$signalType.cellularity'
-  		#else
+  		#if $input.signal == "CN":
+  			--nbcall '$input.nbcall' 
+  			--cellularity '$input.cellularity'
+	                --output '$outputC'
+                        --new_file_path '$outputC.extra_files_path'
+		#else
   			--nbcall '3' 
   			--cellularity '1.0'
-  		#end if
-  		--input '$input' 
-  		--new_file_path '$output.extra_files_path' 
+			--output '$outputF'
+                        --new_file_path '$outputF.extra_files_path'
+		#end if
+  		--input '$input.input_cond' 
   		--outputlog '$outputlog' 
-  		--output '$output' 
   		--log '$log' 
   		--outputgraph '$outputgraph'
   		--graph '$graph' 
   		--method '$method' 
-  		--signalType '$signalType.signal'
+  		--signalType '$input.signal'
   		--user_id '$__user_id__'
   	]]>
   		
   </command>
   <inputs>
-    <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
-	    
-    <param name="method" type="select" label="Segmentation method" help="">
-      <option value="cghseg">cghseg</option>
-      <option value="PELT">PELT</option>
-    </param>
-    
-	<conditional name="signalType">
+	<conditional name="input">
     	<param name="signal" type="select" multiple="false" label="Signal type">
      		<option value="CN">CN</option>
       		<option value="fracB">fracB</option>
     	</param> 
-    	<when value="fracB"/>
+	<when value="fracB">
+	<param name="input_cond" type="data" format="saf" label="Input Signal" help="see below for more information on file format"/>
+	</when>
     	<when value="CN">
-    		
+    <param name="input_cond" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>		
     <param name="nbcall" type="select" label="Number of calling classes" help="The number of levels to be used for calling. Either 3 (loss, normal, gain), 4 (including amplifications), 5 (including double deletions) ">
       <option value="3">3</option>
       <option value="4">4</option>
@@ -50,7 +47,12 @@
     </param>
     <param name="cellularity" type="float" size="5" value="1" min="0" max="1" label="Cellularity" help="Ratio of tumor cells in the sample. Real value between 0 and 1"/>
 	</when>
-    </conditional>
+</conditional>
+
+     <param name="method" type="select" label="Segmentation method" help="">
+      <option value="cghseg">cghseg</option>
+      <option value="PELT">PELT</option>
+    </param>
     <param name="outputgraph" type="select" label="Output figures">
         <option value="TRUE">Yes</option>
         <option value="FALSE">No</option>
@@ -61,11 +63,16 @@
     </param>
   </inputs>       
   <outputs>
-    <data format="scr" name="output" label="segmentation of ${input.name}" />
-    <data format="log" name="log" label="log of segmentation of ${input.name}">
+    <data format="scr" name="outputC" label="segmentation of ${input.input_cond.name}" >
+                  <filter>input['signal']=='CN'</filter>
+        </data>
+        <data format="sar" name="outputF" label="segmentation of ${input.input_cond.name}" >
+                  <filter>input['signal']=='fracB'</filter>
+        </data>	  
+    <data format="log" name="log" label="log of segmentation of ${input.input_cond.name}">
     	<filter>outputlog == "TRUE"</filter>
     </data>
-    <data format="zip" name="graph" label="graph of segmentation of ${input.name}">
+    <data format="zip" name="graph" label="graph of segmentation of ${input.input_cond.name}">
     	<filter>outputgraph == "TRUE"</filter>
     </data>
   </outputs>