# HG changeset patch
# User jeremie
# Date 1404745585 14400
# Node ID af260c953c946a9793514640efa2cea2e4a7cce2
# Parent  42c6b266b39e0d5ec11b290889f32af1d32288a6
Uploaded

diff -r 42c6b266b39e -r af260c953c94 cnvnator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnvnator.xml	Mon Jul 07 11:06:25 2014 -0400
@@ -0,0 +1,40 @@
+<tool id="cnvnator" name="cnvnator" version="0.3">
+	<description></description>
+
+	<command interpreter="python">
+		cnvnator.py
+		-r $inputFastaFile
+		-b $inputBamFile
+		-s $binSize
+		-o1 $outputRawFile
+		-o2 $outputVcfFile
+		$outputRaw
+	</command>
+
+	<inputs>
+		<param format="fasta" name="inputFastaFile" type="data" label="reference file" help="" />
+		<param format="bam" name="inputBamFile" type="data" label="bam file" help="" />
+		<param name="binSize" type="integer" label="bin size" help="" value="100" />
+<!-- 		<conditional name="outputChoice">
+			<param name="outputChoiceSelect" type="select" label="Conditional output">
+				<option value="yes">Yes</option>
+				<option value="no">No</option>
+			</param>
+		</condition> -->
+		<param name="outputRaw" type="boolean" label="output raw?" checked="false" />
+		<param name="outputVcf" type="boolean" label="output vcf?" checked="true" />
+	</inputs>
+
+	<outputs>
+		<data format="tabular" name="outputRawFile" >
+			<filter>outputRaw == false</filter>
+		</data>
+		<data format="vcf" name="outputVcfFile" />
+	</outputs>
+
+	<help>
+
+
+	</help>
+
+</tool>
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