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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 962161e1dde26559d0bc1ce5d7b75d2f354606c5
author iuc
date Mon, 04 Sep 2017 02:47:12 -0400
parents 2aa02d2a6af3
children 78c75f134c16
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<tool id="abricate_list" name="ABRicate List" version="0.7">
    <requirements>
        <requirement type="package" version="0.7">abricate</requirement>
    </requirements>

    <version_command>abricate --version</version_command>

    <command detect_errors="exit_code"><![CDATA[
        abricate --list > '$report'
    ]]></command>

    <inputs>
    </inputs>

    <outputs>
        <data name="report" format="txt" label="${tool.name} - list of databases"/>
    </outputs>

    <tests>
        <test>
            <output name="report" ftype="txt" file="output_list.txt" compare="contains" />
        </test>
    </tests>

    <help><![CDATA[
**What it does**

ABRicate List will list all the antibiotic databases used by ABRicate. The database of these genes is built from ResFinder.
    ]]></help>

    <citations>
        <citation type="bibtex">
@UNPUBLISHED{Seemann2016,
    author = {Seemann, Torsten},
    title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
    year = {2016},
    url = {https://github.com/tseemann/abricate},
}
        </citation>
    </citations>
</tool>