<tool id="complexity_fasta" name="Complexity FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">    
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="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>
    <expand macro="citations" />
</tool>