<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>