<tool id="vcftools_annotate" name="Annotate" version="0.1">
    <description>a VCF dataset with custom filters</description>

    <requirements>
        <requirement type="binary">echo</requirement>
        <requirement type="package" version="0.1.11">vcftools</requirement>
        <requirement type="set_environment">PERL5LIB</requirement>
    </requirements>
    
    <command>
        ## Generate filter file.
        echo "{ tag  => '${tag}', name => '${filter}', desc => '${description}', test => sub { my @t = split('%', @\\$MATCH[0]); return @t[0] $condition ? \\$PASS : \\$FAIL }, }," > f.txt ;

        ## Annotate.
        vcf-annotate -f f.txt ${input} > ${output}
    </command>
    <inputs>
        <param name="input" label="Input" type="data" format="vcf"/>
        <param name="tag" label="Tag name" type="text"/>
        <param name="description" label="Tag description" type="text">
            <sanitizer sanitize="False"/>
        </param>
        <param name="filter" label="Filter name" type="text"/>
        <param name="condition" label="Filter condition" type="text">
            <sanitizer sanitize="False"/>
        </param>
    </inputs>

    <outputs>
        <data name="output" format="vcf"/>
    </outputs>

    <stdio>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <tests>
        <test>
            <param name="input" value="test_in1.vcf" />
            <param name="tag" value="FORMAT/FREQ" />
            <param name="description" value="MinAF [7]"/>
            <param name="filter" value="MinAF" />
            <param name="condition" value=">= 7" />
            <!-- 2 lines diff because command line with full file path is included in output VCF, and
                 it not possible to match full file path.  -->
            <output name="output" file="test_out1.vcf" lines_diff="2" />
        </test>
    </tests>

    <help>
Annotates VCF dataset with custom annotations. For example, if this format tag is used for allele frequency:

##FORMAT=&lt;ID=FREQ,Number=1,Type=String,Description=&quot;Variant allele frequency&quot;&gt;

you can add a filter for allele frequency using &quot;FORMAT/FREQ&quot; as the tag name and the condition &quot;>= [desired allele freq]&quot;

Please see the VCFtools `documentation`__ for help and further information.

.. __: http://vcftools.sourceforge.net/perl_module.html#vcf-annotate
    </help>
</tool>