--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/emboss_5/emboss_newcpgreport.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,44 @@
+<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">
+  <description>Report CpG rich areas</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="window" size="4" type="text" value="100">
+      <label>Window Size</label>
+    </param>
+    <param name="shift" size="4" type="text" value="1">
+      <label>Step size (shift)</label>
+    </param>
+    <param name="minlen" size="4" type="text" value="200">
+      <label>Minimum length</label>
+    </param>
+    <param name="minoe" size="4" type="text" value="0.6">
+      <label>Minimum average observed to expected ratio</label>
+    </param>
+    <param name="minpc" size="4" type="text" value="50.0">
+      <label>Minimum average percentage of G plus C</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="newcpgreport" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="window" value="100"/>
+      <param name="shift" value="1"/>
+      <param name="minlen" value="200"/>
+      <param name="minoe" value="0.6"/>
+      <param name="minpc" value="50.0"/>
+      <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/>
+    </test>
+  </tests>
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html
+  </help>
+</tool>
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