# HG changeset patch
# User fcaramia
# Date 1371446029 14400
# Node ID cf300f1ceeeed0ddce6961c0c5cd16df922c446a
# Parent  32086c82051c08890a51a613b194b89067581842
Uploaded

diff -r 32086c82051c -r cf300f1ceeee baseline.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/baseline.xml	Mon Jun 17 01:13:49 2013 -0400
@@ -0,0 +1,71 @@
+<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>
+|
+
+**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>
+
+