view macros.xml @ 8:97e44e92e5b9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit c7fe7b3a7c6e1f2109868093b9ce5321c2979a24

<macros>
    <token name="@TOOL_VERSION@">0.8.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bandage</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>@HEADLESS@ Bandage --version</version_command>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">bandage</xref>
        </xrefs>
    </xml>
    <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]></token>
    <token name="@BANDAGE_OVERVIEW@">

**Bandage Overview**

Bandage is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others.
De novo assembly graphs contain not only assembled contigs but also the connections between those contigs, which were previously not easily accessible. Bandage visualises assembly graphs, with connections, using graph layout algorithms. Nodes in the drawn graph, which represent contigs, can be automatically labelled with their ID, length or depth. Users can interact with the graph by moving, labelling and colouring nodes. Sequence information can also be extracted directly from the graph viewer. By displaying connections between contigs, Bandage opens up new possibilities for analysing and improving de novo assemblies that are not possible by looking at contigs alone.

Bandage works with Graphical Fragment Assembly (GFA) files. For more information about this file format, see here_

.. _here: https://gfa-spec.github.io/GFA-spec/GFA2.html
    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btv383</citation>
        </citations>
    </xml>
</macros>