# HG changeset patch
# User sblanck
# Date 1618924284 0
# Node ID 4f753bb8681e3847ed2e4033a6d3b14d508187b4
# Parent  3fcbb8030fcc153a2164d686e4f100cfbcf22eee
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"

diff -r 3fcbb8030fcc -r 4f753bb8681e datatypes_conf.xml
--- a/datatypes_conf.xml	Mon Apr 12 14:47:09 2021 +0000
+++ b/datatypes_conf.xml	Tue Apr 20 13:11:24 2021 +0000
@@ -13,6 +13,8 @@
 	<datatype extension="sar" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="false"/>
 	<!-- signal extraction file-->
 	<datatype extension="sef" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
+	<datatype extension="saf" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/>
+	<datatype extension="nzip" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>
 	<!--End MPAgenomics extensions-->     
      </registration>
 </datatypes>
diff -r 3fcbb8030fcc -r 4f753bb8681e extractCN.xml
--- a/extractCN.xml	Mon Apr 12 14:47:09 2021 +0000
+++ b/extractCN.xml	Tue Apr 20 13:11:24 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="extract" name="Extract" version="1.2.0">
+<tool id="extract" name="Extract" version="1.3.0">
   <description>copy number or allele B fraction signal</description>
    <requirements>
         <container type="docker">sblanck/mpagenomicsdependencies</container>
@@ -10,8 +10,6 @@
     --chrom '$chrom'
   	--input '$input'
   	--zip '$zip'
-  	--output '$output' 
-  	--new_file_path '$output.extra_files_path'
   	#if $settings.settingsType == "file":
   		--settings_type '$settings.inputs'
   	#end if
@@ -19,11 +17,15 @@
   		--settings_type 'dataset'
   	#end if
   	#if $settingsSNP.signal == "fracB":
-  		--settings_snp 'TRUE'
+	        --new_file_path '$outputF.extra_files_path'
+	        --output '$outputF'
+		--settings_snp 'TRUE'
   		--settings_tumor '$settingsSNP.tumorcsvFracBsym'
   		--symmetrize 'TRUE'
   	#else
-  		--settings_snp '$settingsSNP.snp'
+	        --new_file_path '$outputC.extra_files_path'
+	        --output '$outputC'
+	        --settings_snp '$settingsSNP.snp'
   		#if $settingsSNP.settingsTumor.settingsTypeTumor == "standard":
   			--settings_tumor 'None'
   		#elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor":
@@ -38,7 +40,7 @@
   </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"/>
+	  <param name="zip" type="data" format="nzip" 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>
@@ -138,7 +140,14 @@
     </param>
   </inputs>
   <outputs>
-	  <data format="sef" name="output" label="signal extraction of ${settingsSNP.signal} of ${input.name}" />
+	  <data format="saf" name="outputF" label="signal extraction of ${settingsSNP.signal} of ${input.name}">
+                <filter>settingsSNP['signal']=='fracB'</filter>
+          </data>
+
+	  <data format="sef" name="outputC" label="signal extraction of ${settingsSNP.signal} of ${input.name}">
+	  	<filter>settingsSNP['signal']=='CN'</filter>
+	</data>
+
     <data format="log" name="log" label="log of signal extraction of ${settingsSNP.signal} of ${input.name}">
     	<filter>outputlog == "TRUE"</filter>
     </data>
diff -r 3fcbb8030fcc -r 4f753bb8681e filter.xml
--- a/filter.xml	Mon Apr 12 14:47:09 2021 +0000
+++ b/filter.xml	Tue Apr 20 13:11:24 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="callfilter" name="Filter" description="segmented and called data" version="1.2.0">
+<tool id="callfilter" name="Filter" description="segmented and called data" version="1.3.0">
    <requirements>
         <container type="docker">sblanck/mpagenomicsdependencies</container>
   </requirements>
@@ -6,43 +6,50 @@
   	<![CDATA[ 
         Rscript 
         ${__tool_directory__}/filter.R 
-  		--input '$input' 
+	        --input '${settingsSNP.input_cond}' 
   		--length '$length' 
   		--probes '$probes' 
-  		--new_file_path '$output.extra_files_path' 
 		 #if $settingsSNP.signal == "fracB":
- 		      --nbcall 'normal'
-                 #else
+		      --nbcall 'normal'
+		      --output '$outputF'
+		      --new_file_path '$outputF.extra_files_path'     
+		 #else
 		      --nbcall '${settingsSNP.nbcall}'
+		      --output '$outputC'
+		      --new_file_path '$outputC.extra_files_path'
 		 
         	 #end if
 		--settings_signal '$settingsSNP.signal' 
-		--output '$output' 
   		--outputlog '$outputlog' 
   		--log '$log'
   	]]>
   </command>
   <inputs>
-    <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/>
-    <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/>
-	<param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/>
-	
-  <conditional name="settingsSNP">
+	   <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="CN">
-		<param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
-      		<option value="double_loss">double loss</option>
-      		<option value="loss">loss</option>
-      		<option value="normal">normal</option>
-      		<option value="gain">gain</option>
-      		<option value="amplification">amplification</option>
-	    	</param>
-	</when>
+                <param name="input_cond" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/>
+                <param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
+                <option value="double_loss">double loss</option>
+                <option value="loss">loss</option>
+                <option value="normal">normal</option>
+                <option value="gain">gain</option>
+                <option value="amplification">amplification</option>
+                </param>
+        </when>
+        <when value="fracB">
+                <param name="input_cond" type="data" format="sar" label="Segmented allele b data file" help="Input file with segments"/>
+        </when>
 
   </conditional>
+
+	  
+	  <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/>
+	<param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/>
+	
     <param name="outputlog" type="select" label="Output log">
         <option value="TRUE">Yes</option>
         <option value="FALSE">No</option>
@@ -50,9 +57,13 @@
   </inputs>
   
   <outputs>
-    <data format="tabular" name="output" label="filter of ${on_string}" />
-    
-	<data format="log" name="log" label="log of filter of ${input.name}">
+    <data format="scr" name="outputC" label="filter of ${settingsSNP.input_cond.name}">
+              <filter>settingsSNP['signal'] == 'CN'</filter>
+          </data>
+           <data format="sar" name="outputF" label="filter of ${settingsSNP.input_cond.name}">
+              <filter>settingsSNP['signal'] == "fracB"</filter>
+          </data>
+	<data format="log" name="log" label="log of filter of ${settingsSNP.input_cond.name}">
     	<filter>outputlog == "TRUE"</filter>
     </data>  
   </outputs>
diff -r 3fcbb8030fcc -r 4f753bb8681e preprocess.xml
--- a/preprocess.xml	Mon Apr 12 14:47:09 2021 +0000
+++ b/preprocess.xml	Tue Apr 20 13:11:24 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="preprocess" name="Data Normalization" version="1.2.0">
+<tool id="preprocess" name="Data Normalization" version="1.3.0">
   <requirements>
       <container type="docker">sblanck/mpagenomicsdependencies</container>
   </requirements>
@@ -72,7 +72,7 @@
   	     doesn't occur. 
   	-->
     <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" />
-    <data format="zip" name="zipresults" label="Results of normalization of ${datasetName}"/>
+    <data format="nzip" name="zipresults" label="Results of normalization of ${datasetName}"/>
     <data format="zip" name="zipfigures" label="Figures of normalization of ${datasetName}">
     	<filter>outputgraph == "TRUE"</filter>	
     </data>    
diff -r 3fcbb8030fcc -r 4f753bb8681e segmentation.xml
--- 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>
diff -r 3fcbb8030fcc -r 4f753bb8681e selectionExtracted.xml
--- a/selectionExtracted.xml	Mon Apr 12 14:47:09 2021 +0000
+++ b/selectionExtracted.xml	Tue Apr 20 13:11:24 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="markersSelection" name="Markers selection" version="1.2.0">
+<tool id="markersSelection" name="Markers selection" version="1.3.0">
    <requirements>
         <container type="docker">sblanck/mpagenomicsdependencies</container>
   </requirements>
@@ -26,10 +26,10 @@
     	<option value="logistic">Logistic</option>
     </param>
    
-	<param name="outputgraph" type="select" label="Output figures">
+	<!--param name="outputgraph" type="select" label="Output figures">
         <option value="TRUE">Yes</option>
         <option value="FALSE">No</option>
-     </param>    
+     </param-->    
     <param name="outputlog" type="select" label="Output log">
         <option value="TRUE">Yes</option>
         <option value="FALSE">No</option>