<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
    <description>Tag somatic mutations in a GEMINI database</description>
    <macros>
        <import>gemini_macros.xml</import>
        <token name="@BINARY@">set_somatic</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        cp "${ infile }" "${ outfile }" &&

        gemini @BINARY@

        #if float($min_depth) >= 0:
            --min-depth $min_depth
        #end if
        
        #if float($min_quality) >= 0:
            --min-qual $min_quality
        #end if

        #if float($min_somatic_score) >= 0:
            --min-somatic-score $min_somatic_score
        #end if

        #if float($max_norm_alt_freq) >= 0:
            --max-norm-alt-freq $max_norm_alt_freq
        #end if

        #if int($max_norm_alt_count) >= 0:
            --max-norm-alt-count $max_norm_alt_count
        #end if

        #if int($min_norm_depth) >= 0:
            --min-norm-depth $min_norm_depth
        #end if

        #if float($min_tumor_alt_freq) >= 0:
            --min-tumor-alt-freq $min_tumor_alt_freq
        #end if

        #if int($min_tumor_alt_count) >= 0:
            --min-tumor-alt-count $min_tumor_alt_count
        #end if

        #if int($min_tumor_depth) >= 0:
            --min-tumor-depth $min_tumor_depth
        #end if

        #if str($chrom).strip():
            --chrom "$chrom"
        #end if 
        "${ outfile }"
]]>
    </command>
    <inputs>

        <expand macro="infile" />
        <param name="min_depth" type="float" value="-1" label="The min combined depth for tumor + normal" help="default: -1 (not set) (--min-depth)"/>
        <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min-qual)"/>
        <param name="min_somatic_score" type="float" value="-1" label="The min somatic score (SSC)" help="default: -1 (not set) (--min-somatic-score)"/>
        <param name="max_norm_alt_freq" type="float" value="-1" label="The max frequency of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-freq)"/>
        <param name="max_norm_alt_count" type="integer" value="-1" min="-1" label="The max count of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-count)"/>
        <param name="min_norm_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the normal sample to believe somatic" help="default: -1 (not set) (--min-norm-depth)"/>
        <param name="min_tumor_alt_freq" type="float" value="-1" label="The minimum frequency of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-freq)"/>
        <param name="min_tumor_alt_count" type="integer" value="-1" min="-1" label="The minimum count of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-count)"/>
        <param name="min_tumor_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the tumor sample to believe somatic" help="default: -1 (not set) (--min-tumor-depth)"/>
        <param name="chrom" type="text" label="A specific chromosome on which to tag somatic mutations" help="e.g. chrom12 (--chrom)" />

    </inputs>
    <outputs>
        <data name="outfile" format="gemini.sqlite" />
    </outputs>
    <tests>
        <test>
            <!-- A very basic test with a nonsensical input db. The example 
                databases that would produce something meaningful are >100 Mbyte -->
            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
            <param name="min_somatic_score" value="5.65"  />
            <output name="outfile" file="gemini_is_somatic_result.db" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Gemini set_somatic sets the flag "is_somatic" by comparing tumor/normal pairs in an already loaded Gemini database. 

]]>
    </help>
    <expand macro="citations"/>
</tool>