comparison abricate.xml @ 4:78c75f134c16 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339

3:6e9aea89e388

<tool id="abricate" name="ABRicate" 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 '$file_input'
        $adv.no_header
        #if $adv.min_dna_id

    <inputs>
        <param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." />
        <section name="adv" title="Advanced options" expanded="False">
            <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
                <option value="argannot">argannot</option>
                <option value="card">card</option>
                <option value="ncbibetalactamase">ncbi betalactamase</option>
                <option value="resfinder" selected="true">resfinder</option>
                <option value="plasmidfinder">plasmidfinder</option>
                <option value="vfdb">vfdb</option>
            </param>
            <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
            <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
        </section>
    </inputs>

        6159.fna  NC_017338.1  39177   41186   mecA_15  1-2010/2010  ===============  0/0   100.00     100.000    resfinder  AB505628
        6159.fna  NC_017338.1  727191  728356  norA_1   1-1166/1167  ===============  0/0   99.91      92.367     resfinder  M97169
        6159.fna  NC_017339.1  10150   10995   blaZ_32  1-846/846    ===============  0/0   100.00     100.000    resfinder  AP004832
    ]]></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@UNPUBLISHED{Seemann2016,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>

4:78c75f134c16

<tool id="abricate" name="ABRicate" version="@VERSION@">
    <description>
        Mass screening of contigs for antimicrobial and virulence genes
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[
        abricate '$file_input'
        $adv.no_header
        #if $adv.min_dna_id

    <inputs>
        <param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." />
        <section name="adv" title="Advanced options" expanded="False">
            <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
                <option value="argannot">ARG-ANNOT</option>
                <option value="card">CARD</option>
                <option value="ecoh">EcOH</option>
                <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option>
                <option value="resfinder" selected="true">Resfinder</option>
                <option value="plasmidfinder">PlasmidFinder</option>
                <option value="vfdb">VFDB</option>
            </param>
            <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
            <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
        </section>
    </inputs>

        6159.fna  NC_017338.1  39177   41186   mecA_15  1-2010/2010  ===============  0/0   100.00     100.000    resfinder  AB505628
        6159.fna  NC_017338.1  727191  728356  norA_1   1-1166/1167  ===============  0/0   99.91      92.367     resfinder  M97169
        6159.fna  NC_017339.1  10150   10995   blaZ_32  1-846/846    ===============  0/0   100.00     100.000    resfinder  AP004832
    ]]></help>

    <expand macro="citations"/>
</tool>