--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_lof_sieve.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,39 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@version@.0">
+    <description>Filter LoF variants by transcript position and type</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">lof_sieve</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far 
+more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool 
+reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence. 
+In addition, it also reports the predicted function of the transcript so that one can segregate candidate 
+LoF variants that affect protein_coding transcripts from processed RNA, etc.
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>