# HG changeset patch
# User fcaramia
# Date 1354495727 18000
# Node ID 073c2382b3afa23b3a252c7bbc14d18076a7c0fb
# Parent  1a5cbabc4cd3ff0e091dbb9605c6a29d0b9ab16a
Uploaded

diff -r 1a5cbabc4cd3 -r 073c2382b3af Contra/baseline.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Contra/baseline.xml	Sun Dec 02 19:48:47 2012 -0500
@@ -0,0 +1,69 @@
+<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>
+  </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>
+|
+
+**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>
+
+