<tool id="phykit_tree_based" name="PhyKit - 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 == "evolutionary_rate"    
            phykit evolutionary_rate $tools.input1 > $evo_rate;
        #elif $tools.tool_selector == "patristic_distances"
            phykit patristic_distances $tools.verbose $tools.input1 > $patristic_distances;
        #elif $tools.tool_selector == "prune_tree"
            phykit prune_tree $tools.input1 $tools.input2
            -o 'out.pruned'
            $tools.keep;
            cp out.pruned ${pruned_tree_out};
        #elif $tools.tool_selector == "robinson_foulds_distance"
            phykit robinson_foulds_distance $tools.input1 $tools.input2 > $rf_distance;
        #elif $tools.tool_selector == "root_tree"
            phykit root_tree $tools.input1 
            -r $tools.input2
            -o 'out.rooted';
            cp out.rooted ${rooted_tree};
        #end if

    ]]></command>
    <inputs>
        <conditional name="tools">
            <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
                <option value="evolutionary_rate">Calculate a tree-based estimation of the evolutionary rate of a gene.</option>
                <option value="patristic_distances">Calculate summary statistics among patristic distances in a phylogeny</option>
                <option value="prune_tree">Prune tips from a phylogeny</option>
                <option value="robinson_foulds_distance">Calculate Robinson-Foulds (RF) distance between two trees</option>
                <option value="root_tree">Root phylogeny using user-specified taxa</option>
            </param>
            <when value="evolutionary_rate">
                <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
            </when>
            <when value="patristic_distances">
                <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
                <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False" label="optional argument to get all distances" />
            </when>
            <when value="prune_tree">
                <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
                <param name="input2" type="data" format="text" multiple="false" label="Single column file with the names of the tips to remove from the phylogeny" optional="false" />
                <param name="keep" type="boolean" truevalue="--keep" falsevalue="" checked="False" label="Instead of pruning tips in list of taxa, keep them" />
            </when>
            <when value="robinson_foulds_distance">
                <param name="input1" type="data" format="newick" multiple="false" label="Tree 1" optional="false" />
                <param name="input2" type="data" format="newick" multiple="false" label="Tree 2" optional="false" />
            </when>
            <when value="root_tree">
                <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
                <param name="input2" type="data" format="text" multiple="false" label="Single column file with taxa names to root the phylogeny on" optional="false" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="evo_rate" format="txt" label="total tree length divided by the number of terminals.">
            <filter>tools['tool_selector']=='evolutionary_rate'</filter>
        </data>
        <data name="patristic_distances" format="txt" label="summary statistics of all tip-to-tip distances in a phylogeny. With the -v option, the first column will have two taxon names separated by a ‘-‘ followed by the patristic distance. Features will be tab separated.">
            <filter>tools['tool_selector']=='patristic_distances'</filter>
        </data>
        <data name="pruned_tree_out" format="newick" label="Pruned phylogeny">
            <filter>tools['tool_selector']=='prune_tree'</filter>
        </data>
        <data name="rf_distance" format="tabular" label="col 1; the plain RF distance and col 2: the normalized RF distance" >
            <filter>tools['tool_selector']=='robinson_foulds_distance'</filter>
        </data>
        <data name="rooted_tree" format="newick" label="Rooted tree">
            <filter>tools['tool_selector']=='root_tree'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="tool_selector" value="evolutionary_rate" />
            <param name="input1" value="12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit.treefile"/>
            <output name="evo_rate" file="test_evo_rate.txt"/>
        </test>
        <test>
            <param name="tool_selector" value="patristic_distances" />
            <param name="input1" value="tree_simple.tre"/>
            <param name="verbose" value="false" />
            <output name="patristic_distances" file="test_tree_simple_pd.txt"/>
        </test>
        <test>
            <param name="tool_selector" value="patristic_distances" />
            <param name="input1" value="tree_simple.tre"/>
            <param name="verbose" value="true" />
            <output name="patristic_distances" file="test_tree_simple_pd_verbose.txt"/>
        </test>
        <test>
            <param name="tool_selector" value="prune_tree" />
            <param name="input1" value="tree_simple.tre"/>
            <param name="input2" value="tree_simple_prune.txt"/>
            <param name="keep" value="false" />
            <output name="pruned_tree_out" file="tree_simple.pruned"/>
        </test>
        <test>
            <param name="tool_selector" value="prune_tree" />
            <param name="input1" value="tree_simple.tre"/>
            <param name="input2" value="tree_simple_prune.txt"/>
            <param name="keep" value="true" />
            <output name="pruned_tree_out" file="tree_simple_keep.pruned"/>
        </test>
        <test>
            <param name="tool_selector" value="robinson_foulds_distance" />
            <param name="input1" value="tree_simple.tre"/>
            <param name="input2" value="tree_simple_other_topology.tre"/>
            <output name="rf_distance" file="test_tree_simple_rfd.txt"/>
        </test>
        <test>
            <param name="tool_selector" value="root_tree" />
            <param name="input1" value="tree_simple.tre"/>
            <param name="input2" value="tree_simple.outgroup.txt"/>
            <output name="rooted_tree" file="tree_simple.tre.rooted"/>
        </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#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).

Tree-based commands
===================
evolutionary_rate (alias: evo_rate)
    - reports a tree-based estimation of evolutionary rate for a gene
patristic_distances (alias: pd)
    - calculate all pairwise distances between tips in a tree
prune_tree (alias: prune)
    - prune taxa from a phylogeny
robinson_foulds_distance (alias: rf_distance; rf_dist; rf)
    - calculates Robinson-Foulds distance between two trees
root_tree (alias: root; rt)
    - roots tree on user-specified taxa or taxon

    ]]></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>