<tool id="PlasFlow" name="PlasFlow" version="1.0">
    <description>Prediction of plasmid sequences in metagenomic contigs</description>
    <requirements>
        <requirement type="package" version="1.1.0">plasflow</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
PlasFlow.py
--input '$readFile'
--output 'output'
--threshold '$threshold'
    ]]></command>
    <inputs>
        <param name="readFile" type="data" format="fastq,fasta" optional="true" label="Sequence Reads" />
        <param argument="threshold" type="float" value="0.7" label="Threshold for porbability filtering"/>
    </inputs>
    <outputs>
        <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" />
        <data name="chromosomes" from_work_dir="output_chromosomes.fasta" format="fasta" label="${tool.name} on ${on_string}: Chromosomes" />
        <data name="plasmids" from_work_dir="output_plasmids.fasta" format="fasta" label="${tool.name} on ${on_string}: Plasmids" />
        <data name="unclassified" from_work_dir="output_unclassified.fasta" format="fasta" label="${tool.name} on ${on_string}: Unclassified" />
    </outputs>
    <tests>
        <test>
            <param name="readFile" value="test.fasta"/>
            <param name="threshold" value="0.7"/>
            <output name="probability_table" value="output"/>
            <output name="chromosomes" value="output_chromosomes.fasta"/>
            <output name="plasmids" value="output_plasmids.fasta"/>
            <output name="unclassified" value="output_unclassified.fasta"/>
        </test>
    </tests>
    <help><![CDATA[
PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. It relies on the neural network models trained on full genome and plasmid sequences and is able to differentiate between plasmids and chromosomes with accuracy reaching 96%. It outperforms other available solutions for plasmids recovery from metagenomes and incorporates the thresholding which allows for exclusion of incertain predictions. PlasFlow has been published in Nucleic Acids Research
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkx1321</citation>
    </citations>
</tool>