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

        ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' &&

        quasitools complexity bam '$ref_file' '$input_bam'  $k -f '$filter_size' -o output.csv

    ]]></command>
    <inputs>
        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
        <param name="input_bam" type="data" format="bam" optional="false" label="BAM file" />
        <param name="k" type="integer" label="k-mer size" value="0" min="0" />
        <param name="filter_size" type="integer" label="Filter size" value="0" min="0" />
    </inputs>
    <outputs>
        <data format="csv" name="output" from_work_dir="output.csv" />
    </outputs>
   <tests>
        <test>
            <param name="ref_file" value="generated.fasta" />
            <param name="input_bam" value="generated.bam" />
	    <param name="k" value="200" />
	    <param name="filter_size" value="0" />
            <output name="output" >
                <assert_contents>
                    <has_text text="Position" />
                    <has_text text="0" />
                </assert_contents>
            </output>
        </test>
    </tests>
   
    <help><![CDATA[
Quasispecies Complexity
=======================

Calculates various quasispecies complexity measures on next generation sequenced data from a BAM file and it's corresponding reference file.

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>