<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>