annotate macro.xml @ 6:1920244e2895 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit b9e8ae9eeeff6fb23e25eca3d4a89323c7f37c33

<macros>
    <token name="@TOOL_VERSION@">3.11.26</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">21.05</token>
    <xml name="version_command">
        <version_command><![CDATA[amrfinder --version]]></version_command>
    </xml>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">amrfinderplus</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">ncbi-amrfinderplus</requirement>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41598-021-91456-0</citation>
        </citations>
    </xml>

    <xml name="nucl_input" token_option="">
        <param name="nucleotide_input" type="data" optional="@OPTION@" format="fasta" label="Input nucleotide sequence file" help="Select the nucleotide sequence file to be analyzed"/>
    </xml>
    <xml name="prot_input" token_option="">
        <param name="protein_input" type="data" optional="@OPTION@" format="fasta" label="Input protein sequence file" help="Select the protein sequence file to be analyzed"/>
    </xml>
    <xml name="annotation_type" token_option="">
        <param name="gff_annotation" type="data" format="gff3" optional="@OPTION@" multiple="false" label="GFF file for protein locations" help="Protein id should be in the attribute Name=id (9th field) of the rows with type CDS or gene (3rd field)"/>
        <param argument="--annotation_format" type="select" optional="@OPTION@" label="Annotation file format" help="Select the annotation format type (eg. bakta or prokka tool, genbank format (default: genbank)">
            <option value="bakta">Bakta</option>
            <option value="genbank">Genbank</option>
            <option value="microscope">Microscope</option>
            <option value="patric">Patric</option>
            <option value="prokka">Prokka</option>
            <option value="pseudomonasdb">Pseudomonasdb</option>
            <option value="rast">Rast</option>
            <option value="standard">Standard</option>
        </param>
    </xml>
</macros>