comparison abricate_list.xml @ 0:862f5a86854d draft

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0:862f5a86854d

<tool id="abricate_list" name="ABRicate List" version="0.1.0">
    <requirements>
        <requirement type="package" version="0.3">abricate</requirement>
        <requirement type="package" version="5.18.1">perl</requirement>
        <requirement type="package" version="2.2.31">blast+</requirement>
    </requirements>

    <version_command>abricate --version</version_command>

    <command detect_errors="exit_code"><![CDATA[
        abricate --list 2> "$report"
    ]]></command>

    <inputs>

    </inputs>

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

    <tests>
        <test>
            <output name="report" ftype="txt" file="output_list.txt" />
        </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        @UNPUBLISHED{Seemann2016,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 T",
        title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
        year = "2016",
        note = "https://github.com/tseemann/abricate"}
      </citation>
    </citations>
</tool>