view scagaire.xml @ 0:f9d845c8d925 draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/scagaire commit d581c0ded2cfa7dde2d501c5368b055bd7333eb1"

<tool id="scagaire" name="scagaire" version="@VERSION@">
    <description>Filter AMR results by species</description>
    <macros>
        <token name="@VERSION@">0.0.4</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">scagaire</requirement>
    </requirements>
    <version_command>scagaire --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set $clean_species = re.sub("_"," ",$scagaire_species.fields.name)
        scagaire
        -n $db_name
        #if str($amr_type) != "auto"
            -t $amr_type
        #end if
        '$clean_species'
        -m $minimum_occurances
        $debug
        $verbose
        $amr > $output
    ]]>    </command>

    <inputs>
        <param name="amr" type="data" format="tabular,text" label="Select AMR result"/>
        <param name="amr_type" type="select" optional="false" label="Source of AMR results">
            <option value="auto">auto</option>
            <option value="abricate">abricate</option>
            <option value="rgi">rgi</option>
            <option value="staramr">staramr</option>
        </param>
        <param name="db_name" type="select" optional="false" label="Database">
            <option value="argannot">argannot</option>
            <option value="card">card</option>
            <option value="ncbi">ncbi</option>
            <option value="plasmidfinder">plasmidfinder</option>
            <option value="resfinder" selected="True">resfinder</option>
            <option value="vfdb">vfdb</option>
        </param>
        <!-- DATABASE INPUT-->
        <param label="Select a species" name="scagaire_species" type="select">
            <options from_data_table="scagaire_species">
                <validator message="No species is available" type="no_options" />
            </options>
        </param>
        <param name="minimum_occurances" type="integer" min="0" value="0" label="Minimum number of occurances of a gene in the database"/>
        <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Turn on debugging" />
        <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on verbose output" />
    </inputs>

    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string} Output"/>
        <data name="summary" format="tabular" label="${tool.name} on ${on_string} Summary" from_work_dir="gene_summary.tsv"/>
        <data name="log" format="text" label="${tool.name} on ${on_string} Log">
            <filter>debug is True</filter>
        </data>
    </outputs>

    <help><![CDATA[

    Documentation can be found at `<https://github.com/quadram-institute-bioscience/scagaire>`_.

    ]]>    </help>
</tool>