view graphlan_annotate.xml @ 0:c5746c07ca5e draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty

<tool id="graphlan_annotate" name="Modify an input tree for GraPhlAn" version="0.1.0">

    <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[
python \${GRAPHLAN_DIR}/graphlan_annotate.py -v
]]>
    </version_command>

    <command>
<![CDATA[        
        python \${GRAPHLAN_DIR}/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="text" name="output_tree" 
            label="${tool.name} on ${on_string}: Tree in PhyloXML" />
    </outputs>

    <tests>
        <test>
        </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>