<tool id="complexity" name="Complexity" version="0.5.1">
    <description>measures the complexity of the quasispecies reads</description>
    <requirements>
          <requirement type="package" version="0.5.1">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        quasitools complexity $input_fasta > complexity.txt

    ]]></command>
    <inputs>
        <param name="input_fasta" type="data" format="fasta" optional="false" label="Aligned FASTA Input" />
    </inputs>
    <outputs>
        <data format="txt" label="Complexity" name="output_complexity" from_work_dir="complexity.txt" />
    </outputs>

    <tests>
        <test>
            <param name="input_fasta" value="msa.fasta" />
            <output name="output_complexity">
                <assert_contents>
                    <has_text text="Number of haplotypes (H) : 8" />
                    <has_text text="Mutation Frequency (Mfe) : 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>