<tool id="callfilter" name="Filter" description="segmented and called data" version="1.3.0">
   <requirements>
        <container type="docker">sblanck/mpagenomicsdependencies</container>
  </requirements>
  <command>
  	<![CDATA[ 
        Rscript 
        ${__tool_directory__}/filter.R 
	        --input '${settingsSNP.input_cond}' 
  		--length '$length' 
  		--probes '$probes' 
		 #if $settingsSNP.signal == "fracB":
		      --nbcall 'normal'
		      --output '$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 '$settingsSNP.signal' 
  		--outputlog '$outputlog' 
  		--log '$log'
  	]]>
  </command>
  <inputs>
	   <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="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>
    </param>
  </inputs>
  
  <outputs>
    <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>
 
  <stdio>
    <exit_code range="1:"   level="fatal"   description="See logs for more details" />
   </stdio>
   <help>
   	
**What it does**
   	    	
This tool filters results obtained by the segmentation and calling tool.

-----

Input/Output file:
  	
*A tabular text file containing 7 columns:*
	
	- sampleNames: Name of the 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;`_
  
 </help>
   	</tool>