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+++ b/segmentFracB.xml	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,178 @@
+<tool id="segFracB" name="Segmentation of allele B fraction " force_history_refresh="True" version="1.0.0">
+  <description></description>
+  <command>
+    <![CDATA[ 
+        Rscript
+        ${__tool_directory__}/segmentFracB.R  
+  		--chrom '$chrom' 
+  		--input '$input' 
+  		--output '$output' 
+  		--new_file_path '$__new_file_path__'
+  		#if $settings.settingsType == "file":
+  			--settings_type '$settings.inputs'
+  		#end if
+  		#if $settings.settingsType == "dataset":
+  			--settings_type '$settings.settingsType'
+  		#end if
+  		--output_graph '$outputgraph' 
+  		--zip_figures '$zipfigures'
+  		--settings_tumor '$tumorcsv'
+  		--outputlog '$outputlog' 
+  		--log '$log' 
+  		--userid '$__user_id__' 
+  		--method '$method'
+  	]]>
+  </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>
+    
+    <param name="tumorcsv" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/>
+        
+              
+    <!--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="leave 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="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>
+    </param>
+    <param name="outputlog" type="select" label="Output log">
+        <option value="TRUE">Yes</option>
+        <option value="FALSE">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="sar" name="output" label="allele B fraction segmentation of ${input.name}" />
+    <data format="zip" name="zipfigures" label="allele B fraction segmentation figures of ${input.name}">
+    	<filter>outputgraph == "TRUE"</filter>	
+    </data>
+    <data format="log" name="log" label="log of allele B fraction segmentation 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 segmentation.
+
+-----
+
+**What it does**     	
+This tool segments allele B fraction extracted from the previously normalized data. This tools works only on normal-tumor study.
+	
+Outputs:
+  	
+*A tabular text file containing 6 columns which describe all the segment (1 line per segment):*
+	
+	- sampleNames: Name of the file.
+	- chrom: The chromosome of the segment.
+	- chromStart: The starting position (in bp) of the segment. This position is not included in the segment.
+	- chromEnd: The 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.
+	  		
+*A .zip file containing all the figures (optionnal)*
+	
+-----
+  		  		
+**Normal-tumor csv files**
+     	
+Normal-tumor csv file is required to segment Allele B fraction, because naive genotyping is based on normal samples :
+
+	- 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;`_
+	
+If segmentation is performed with PELT, please 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;`_
+	
+</help>
+</tool>
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