view macros.xml @ 5:d8b1027d6ce0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 7823462e83ff5efbcfd3161f7d471fd07da51611"

<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>