<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>perform sample-wise gene-level burden calculations</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">burden</token>
    </macros>
    <command>
<![CDATA[
        gemini @BINARY@
          --cases $cases
          --controls $controls
            $save_tscores
            $nonsynonymous
            $calpha
            --permutations $permutations
            #if float( str($min_aaf) ) >= 0.0:
                --min-aaf $min_aaf
            #end if
            #if float( str($max_aaf) ) >= 0.0:
                --max-aaf $max_aaf
            #end if
            "${ infile }"
            > "${ outfile }"
]]>

    </command>
    <expand macro="stdio" />
    <inputs>
        <expand macro="infile" />

        <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
        <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>

        <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" 
            label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>

        <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False" 
            label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
        <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False" 
            label="Run the C-alpha association test" help="(--calpha)"/>
        <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included" 
            help="(--min-aaf)">
            <!--validator type="in_range" min="0.0"/-->
        </param>
        <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included" 
            help="(--max-aaf)">
            <!--validator type="in_range" min="0.0"/-->
        </param>

        <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test" 
            help="(--permutations)">
            <validator type="in_range" min="0"/>
        </param>

    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
**What it does**

The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. 
By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample.

$ gemini burden test.burden.db
gene    M10475  M10478  M10500  M128215
WDR37   2       2       2       2
CTBP2   0       0       0       1
DHODH   1       0       0       0

@CITATION@
    </help>
    <expand macro="citations">
        <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
    </expand>
</tool>