--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_to_fasta.xml	Thu Mar 26 20:11:34 2015 -0400
@@ -0,0 +1,52 @@
+<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.0">
+	<requirements>
+        <container type="docker">iracooke/protk-1.4.1</container>		
+	    <requirement type="package" version="1.4">protk</requirement>
+   </requirements>
+
+	<description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>
+
+	<command>
+		augustus_to_proteindb.rb $gff_file -o $output $coords
+	</command>
+
+
+
+
+	<stdio>
+		<exit_code range="1:"   level="fatal"   description="Failure" />
+	</stdio>
+
+	<inputs>	
+		<param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" />
+		<param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" />
+	</inputs>
+
+	<outputs>
+		<data format="fasta" name="output" />
+	</outputs>
+
+	<tests>
+	  <!-- Just test that the tool runs and produces vaguely correct output -->
+	  <test>
+	      <param name="gff_file" value="augustus_sample.gff" format="gff3"/>
+	      <output name="output" file="augustus_sample.fasta" format="fasta"/>
+	  </test>
+	</tests>
+
+
+  <help>
+
+**What it does**
+
+Extract proteins from gff3 and encode genomic coordinates in the fasta header.
+Currently this only works with gff3 generated using the Augustus gene finder
+
+----
+
+**References**
+
+
+  </help>
+
+</tool>