<tool id="edu.tamu.cpt.blast.blasttab_dice_filter" name="Blast Tabular Dice Filter" version="19.1.0.0">
    <description>removes low-dice blast results</description>
    <macros>
        <import>macros.xml</import>
        <import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/blasttab_dice_filter.py'
@BLAST_TSV@
--min_dice '$min_dice'
> '$output']]></command>
    <inputs>
        <expand macro="blast_tsv"/>
        <param label="Minimum dice score" help="Blast results with a dice score below this value will be removed" name="min_dice" type="float" value="0.5" min="0.0" max="1.0"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="blast_tsv" value="T7_NT_BLAST.tabular"/>
            <param name="min_dice" value="0.2"/>
            <output name="output" file="T7_NT_BLAST_FILTERED.tabular"/>
        </test>
        <test>
            <param name="blast_tsv" value="results.tsv"/>
            <param name="min_dice" value="0.5"/>
            <output name="output" file="results.diced.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Filters your tabular BLAST results based on a dice score thresholding process.

**How it works**

The tool processes BLAST results line by line, at each line calculating the dice score. 
The equation for the dice score is as follows::

	2 * number of identical matches / (query sequence length + subject sequence length)

The denominator normalizes the score by accounting for the length of both sequences. A 
pairwise alignment is required to have between 50-100% identity. 

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