# HG changeset patch
# User ahosny
# Date 1470511197 14400
# Node ID 8216e150d1aacb4d7200b798bc65ece2e03f88d9
# Parent  aca5f8ee65e4f5d0d65caecc561ba9613bf251df
initial CNV-Sim tool definition (0.9.0)

diff -r aca5f8ee65e4 -r 8216e150d1aa cnv_sim.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv_sim.xml	Sat Aug 06 15:19:57 2016 -0400
@@ -0,0 +1,31 @@
+<tool id="cnv_sim" name="Simulate CNV" version="0.9.0">
+    <description>in NGS short reads </description>
+    <command interpreter="python" detect_errors="exit_code">
+        #if $type.simulation_type=="whole_genome"
+            cnv-sim.py genome $reference
+        #else
+            cnv-sim.py exome $reference $target
+        #end if
+    </command>
+    <inputs>
+        <conditional name="type">
+            <param name="simulation_type" type="select" label="Simulation Type">
+                <option value="whole_genome">CNV Simulation in Whole Genome</option>
+                <option value="whole_exome">CNV Simulation in Exome Regions</option>
+            </param>
+            <when value="whole_genome">
+                <param format="fasta" name="reference" type="data" label="Reference Genome"/>
+            </when>
+            <when value="whole_exome">
+                <param format="fasta" name="reference" type="data" label="Reference Genome"/>
+                <param format="bed" name="target" type="data" label="Target Regions"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bed" name="cnv_list" from_work_dir="test/CNVList.bed"/>
+    </outputs>
+    <help>
+        This tool generates artificial NGS short reads in FASTQ format afficted by Copy Number Variations.
+    </help>
+</tool>
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