<tool id="parse_mito_blast" name="Parse mitochondrial blast" version="@TOOL_VERSION@" profile="21.05">
    <description>overlap-conscious coverage calculation between scaffold-accession number pairs from blast output</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">parse_mito_blast</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
parse_mito_blast.py
    --blastout '$blastout' 
]]>
    </command>
    <inputs>
        <param argument="blastout" type="data" format="tabular" label="Tabular file generated by mito-blast"/>
    </inputs>
    <outputs>
        <data name="cov_report" format="tabular" from_work_dir="cov_report.tsv" label="${tool.name} on ${on_string}" />
        <data name="mito_scaff_names" format="txt" from_work_dir="mito_scaff_names.txt" label="contaminant scaffolds on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="blastout" value="test_input.tsv" />
            <output name="cov_report" file="test_cov_report.tsv" ftype="tabular" /> 
            <output name="mito_scaff_names" file="test_mito_scaff_names.txt" ftype="txt" />
        </test>
    </tests>
    <help><![CDATA[
	
	This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output \
	all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
	collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
	account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
	sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold /
	(sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
	identity to a mitochondrial subject sequence. To use, pass a format 6 blast output (--blastout) and the desired name of the report. 

	NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' /
	and will be sensitive to this order. 
    ]]>
    </help>
    <citations>
	    <citation type="bibtex">
           @misc{Danecek_et_al,
           Author={Danecek, P., Schiffels, S., Durbin, R.},
           title={Multiallelic calling model in bcftools (-m)},
           url = {http://samtools.github.io/bcftools/call-m.pdf},}
        </citation>
    </citations>
</tool>