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changeset 3:cf300f1ceeee draft

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Uploaded
author fcaramia
date Mon, 17 Jun 2013 01:13:49 -0400
parents 32086c82051c
children cd31a9b4744e
files baseline.xml
diffstat 1 files changed, 71 insertions(+), 0 deletions(-) [+]
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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>
+|
+
+**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>
+
+