--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_stats.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,57 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Compute useful variant statistics</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">stats</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+            $stats_type
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <param name="stats_type" type="select" label="Studying ..." help="">
+            <option value="--tstv">Compute the transition and transversion ratios for the snps (--tstv)</option>
+            <option value="--tstv-coding">Compute the transition/transversion ratios for the snps in the coding regions (--tstv-coding)</option>
+            <option value="--tstv-noncoding">Compute the transition/transversion ratios for the snps in the non-coding regions (--tstv-noncoding)</option>
+            <option value="--snp-counts">Compute the type and count of the snps (--snp-counts)</option>
+            <option value="--sfs">Calculate the site frequency spectrum of the variants (--sfs)</option>
+            <option value="--mds">Compute the pair-wise genetic distance between each sample (--mds)</option>
+            <option value="--vars_by_sample">Return the total variants per sample, sum of homozygous and heterozygous variants (--vars-by-sample)</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+The stats tool computes some useful variant statistics for a GEMINI database.
+
+
+$ gemini stats --summarize "select * from variants where in_dbsnp=1 and chrom='chr1'" my.db
+sample  total   num_het num_hom_alt
+M10475  1       1       0
+M128215 1       1       0
+M10478  2       2       0
+M10500  2       1       1
+
+
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>