<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>
        <expand macro="infile" />

        <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" />
    </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>