<tool id="phykit_alignment_tree_based" name="PhyKit - Alignment- and tree-based functions" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="1.11.7">phykit</requirement>
    </requirements>
     <command detect_errors="exit_code"><![CDATA[    
        #if $tools.tool_selector == "treeness_over_rcv"    
            phykit treeness_over_rcv -a $tools.input1 -t $tools.input2 > $treeness_rcv;
        #end if
        

    ]]></command>
    <inputs>
        <conditional name="tools">
            <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
                <option value="treeness_over_rcv">Calculate treeness/RCV for a given alignment and tree.</option>
            </param>
            <when value="treeness_over_rcv">
                <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" />
                <param name="input2" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="treeness_rcv" format="tabular" label="Three tab delimited values: col1: treeness/RCV col2: treeness col3: RCV" >
            <filter>tools['tool_selector']=='treeness_over_rcv'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="tool_selector" value="treeness_over_rcv" />
            <param name="input1" value="simple.fa"/>
            <param name="input2" value="tree_simple.tre"/>
            <output name="treeness_rcv" file="test_treeness_over_rcv.txt"/>
        </test>
    </tests>
    <help><![CDATA[

Version: 1.11.3
Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096
Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#alignment-and-tree-based-functions
Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675

PhyKIT helps process and analyze multiple sequence alignments and phylogenies.

Generally, all functions are designed to help understand the contents of alignments
(e.g., gc content or the number of parsimony informative sites) and the shape
of trees (e.g., treeness, degree of violation of a molecular clock).


Alignment- and tree-based commands
==================================
treeness_over_rcv (alias: toverr)
    - calculates treeness/rcv, treeness, and rcv

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubPhyKIT,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {PhyKIT},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/JLSteenwyk/PhyKIT},
}</citation>
    </citations>
</tool>