diff proteindb_from_gff3.xml @ 0:9a0d14f0f249 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteindb_from_gff3.xml	Sat Jun 14 18:09:19 2014 -0400
@@ -0,0 +1,43 @@
+<tool id="proteindb_from_gff3" name="Extract proteins from gff3" version="1.0.1">
+	<requirements>
+	    <requirement type="package" version="1.3">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>
+
+
+  <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>