<tool id="graphlan_annotate" name="Modify an input tree for GraPhlAn" version="1.0">

    <description></description>

    <requirements>
        <requirement type="package" version="1.66">biopython</requirement>
        <requirement type="package" version="1.4">matplotlib</requirement>
        <requirement type="package" version="1.0">graphlan</requirement>
    </requirements>

    <stdio>
    </stdio>

    <version_command>
<![CDATA[
graphlan_annotate.py -v
]]>
    </version_command>

    <command>
<![CDATA[        
        graphlan_annotate.py
            #if $annot
                --annot $annot
            #end if

            $input_tree
            $output_tree
]]>
    </command>

    <inputs>
        <param name="input_tree" type="data" format="txt" label="Input tree" 
            help="Newick, Nexus, PhyloXML or plain text"/>

        <param name="annot" type="data" format="txt" label="Annotation file 
            (Optional)" help="(--annot)" optional="True"/>
    </inputs>

    <outputs>
        <data format="txt" name="output_tree" 
            label="${tool.name} on ${on_string}: Tree in PhyloXML" />
    </outputs>

    <tests>
        <test>
            <param name="input_tree" value="input_tree.txt" />
            <param name="annot" value="input_annotation.txt" />
            <output name="output_tree" value="output_modified_tree.txt" />
        </test>
    </tests>

    <help><![CDATA[

**What it does**

GraPhlAn is a software tool for producing high-quality circular 
representations of taxonomic and phylogenetic trees. GraPhlAn focuses on 
concise, integrative, informative, and publication-ready representations of 
phylogenetically- and taxonomically-driven investigation.

`graphlan_annotate` modifies any input tree (in any of the three standard format) 
adding additional information regarding structural or graphical aspects of the tree 
(like colors and style of the taxa, labels, shadows, heatmaps, ...).

For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.

    ]]></help>

    <citations>
    </citations>
</tool>