--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation.xml	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,114 @@
+<tool id="segmentation" name="Segmentation and calling" force_history_refresh="True" version="1.1.0">
+  <description>of a previously normalized signal</description>
+  <requirement type="package" version="1.1.2">mpagenomics</requirement>
+  <command>
+    <![CDATA[ 
+        Rscript 
+        ${__tool_directory__}/segmentation.R 
+  		#if $signalType.signal == "CN":
+  			--nbcall '$signalType.nbcall' 
+  			--cellularity '$signalType.cellularity'
+  		#else
+  			--nbcall '3' 
+  			--cellularity '1.0'
+  		#end if
+  		--input '$input' 
+  		--new_file_path '$__new_file_path__' 
+  		--outputlog '$outputlog' 
+  		--output '$output' 
+  		--log '$log' 
+  		--outputgraph '$outputgraph'
+  		--graph '$graph' 
+  		--method '$method' 
+  		--signalType '$signalType.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">
+    	<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="CN">
+    		
+    <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>
+      <option value="5">5</option>
+    </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>
+    <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="scr" name="output" label="segmentation of ${input.name}" />
+    <data format="log" name="log" label="log of segmentation of ${input.name}">
+    	<filter>outputlog == "TRUE"</filter>
+    </data>
+    <data format="pdf" name="graph" label="graph of segmentation of ${input.name}">
+    	<filter>outputgraph == "TRUE"</filter>
+    </data>
+  </outputs>
+  <stdio>
+    <exit_code range="1:"   level="fatal"   description="See logs for more details" />
+   </stdio>
+  <help>
+
+**What it does**     	
+This tool segments normalized profiles provided by the user and labels segments found in the copy-number profiles.
+	
+Input format:
+  	
+*A tabular text file containing 3 fixed columns and 1 column per sample:*
+	
+	- chr: Chromosome.
+	- position: Genomic position (in bp)
+  	- probeName: Probes names.
+  	- One column per sample which contains the copy number profile for each sample
+ 
+Output format:
+  	
+*A tabular text file containing 7 columns which describe all the segments (1 line per segment):*
+	
+	- sampleNames: Column names corresponding to samples in the input file.
+  	- chrom: Chromosome of the segment.
+	- chromStart: Starting position (in bp) of the segment. This position is not included in the segment.
+	- chromEnd: Ending position (in bp) of the segment. This position is included in the segment.
+	- probes: Number of probes in the segment.
+	- means: Mean of the segment.
+	- calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”).
+    
+-----
+  		
+**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;`_
+  	
+If segmentation is performed with PELT, please also cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. &lt;http://arxiv.org/abs/1101.1438&gt;`_
+
+If segmentation is performed by cghseg, please cite	`Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. &lt;http://www.ncbi.nlm.nih.gov/pubmed/15705208&gt;`_ ,
+and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. &lt;http://arxiv.org/abs/1004.0887&gt;`_	
+
+When using the labels of the segments, please cite CGHCall `M. A. van de Wiel, K. I. Kim, S. J. Vosse, W. N. van Wieringen, S. M. Wilting, and B. Ylstra. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics, 23(7):892–894, 2007. &lt;http://bioinformatics.oxfordjournals.org/content/23/7/892.abstract&gt;`_
+	
+</help>
+</tool>