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<tool id="baseline_tool" name="Baseline" version="1.0.0">
  <description>: Control files for Contra</description>
  <requirements>
	<requirement type="package" version="2.17.0">bedtools</requirement>
	<requirement type="package" name="samtools" version="0.1.18">samtools</requirement>
	<requirement type="package" name="contra" version="2.0.4">contra</requirement>
  </requirements>
  <command interpreter="perl">
    
	baseline_wrapper.pl
	
	##Required files
	"PLAYEROPTION::-t=$target_file"
	
	#for $group in $file_group
		"BAMLISTENTRY::${group.bam}"
	#end for
	
	"PLAYEROPTION::--name=$sampleName"
	"PLAYEROPTION::--trim=$trim"
	
	##File to generate the bam list
	"BASELINEOUTPUT::$baseline_output"
  </command>
	<inputs>
		<param name="target_file" type="data" format="bed" help="" optional="false" />		
		<repeat name="file_group" title="Bam file">
			<param format="bam" name="bam" type="data" label="BAM File" help=""/>
		</repeat>
		<param name="sampleName" value="baseline" type="text"  optional="true" />
		<param name="trim"  type="float" value="0.2" optional="true" />

		
	</inputs>
	<outputs>
		<data name="baseline_output" title="Baseline Output"  format="tabular" type="data"  label="Baseline_Control.txt" />
	</outputs>
	<help>
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**Reference**
	http://contra-cnv.sourceforge.net/

-----

**What it does**

Creating a baseline control from multiple samples is can be useful when a matched control is not available. In the CONTRA download page, we have provided several baseline files for some of the platforms that we have tried. Alternatively, the “baseline.py” script that comes with CONTRA can be used to generate a custom baseline file. 

-----
 
**Parameters**

::

  -t, --target          Target region definition file [REQUIRED] [BED format] 

  -f, --files           Files to be converted to baselines [REQUIRED] [BAM] 

  -o, --output          Output folder [REQUIRED] 

  -c, --trim            Portion of outliers to be removed before calculating 
                        average [Default: 0.2]
                        
  -n, --name            Output baseline file name [Default: baseline] 


	</help>
</tool>