<tool id="complexity_fasta" name="Complexity FASTA" version="0.7.0">    
    <requirements>
        <requirement type="package" version="0.7.0">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        quasitools complexity fasta '$input_fasta' -o output.csv

    ]]></command>
    <inputs>
        <param name="input_fasta" type="data" format="fasta" optional="false" label="input file" />  
    </inputs>
    <outputs>
        <data format="csv" name="output" from_work_dir="output.csv" />
    </outputs>
    <tests>
        <test>
            <param name="input_fasta" value="msa.fasta" />
            <output name="output">
                <assert_contents>
                    <has_text text="Number of Haplotypes" />
		    <has_text text="8" />
                    <has_text text="0.75" />
                </assert_contents>
            </output>
        </test>
    </tests>
   
    <help><![CDATA[
Quasispecies Complexity
=======================

Measure the complexity of quasispecies reads using a variety of measures. The input must be an aligned FASTA file, representing a particular reqion of quasispcies from which to measure the complexity.

The measures of complexity are taken from the following work:

Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.


]]></help>
    <citations>
		<citation type="bibtex">
			@misc{GitHubquasitoolscomplexity,
			title = {quasitools complexity},
			publisher = {phac-nml},
			journal = {GitHub repository},
			url = {https://github.com/phac-nml/quasitools},
			}
		</citation>
	</citations>
</tool>