comparison abricate.xml @ 8:b734db305578 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"

7:4efdca267d51

    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)

        ln -sf '${file_input}' ${sample_name} &&
        
        abricate ${sample_name}
        $adv.no_header
        #if $adv.min_dna_id
            --minid=$adv.min_dna_id
        #end if
        --db=$adv.db
        > '$report'
    ]]></command>

                <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>

    <outputs>
        <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />

            <param name="file_input" value="MRSA0252.fna"/>
            <param name="db" value="card"/>
            <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
        </test>

        <!-- Advanced test 4 - Min DNA ID 100 -->
        <test>
            <param name="file_input" value="MRSA0252.fna"/>
            <param name="min_dna_id" value="100"/>
            <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
        </test>

        <!-- Filetype test 5 - input a gbk -->
        <test>
            <param name="file_input" value="test.gbk"/>
            <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
        </test>

8:b734db305578

    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)

        ln -sf '${file_input}' ${sample_name} &&

        abricate ${sample_name}
        $adv.no_header
        #if $adv.min_dna_id
            --minid=$adv.min_dna_id
        #end if
        #if $adv.min_cov
            --mincov=$adv.min_cov
        #end if
        --db=$adv.db
        > '$report'
    ]]></command>

                <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>
                <option value="megares">megares</option>
                <option value="ecoli_vf">Ecoli_VF</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="80" min="0" max="100" optional="true" label="Minimum DNA %identity" />
            <param name="min_cov" argument="--mincov" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %coverage" />
        </section>
    </inputs>

    <outputs>
        <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />

            <param name="file_input" value="MRSA0252.fna"/>
            <param name="db" value="card"/>
            <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
        </test>

        <!-- Advanced test 4 - Changed DB to megares -->
        <test>
            <param name="file_input" value="MRSA0252.fna"/>
            <param name="db" value="megares"/>
            <output name="report" ftype="tabular" file="output_db-megares.txt" compare="contains"/>
        </test>

        <!-- Advanced test 5 - Min DNA ID 100 -->
        <test>
            <param name="file_input" value="MRSA0252.fna"/>
            <param name="min_dna_id" value="100"/>
            <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
        </test>

        <!-- Advanced test 6 - Min Coverage 100 -->
        <test>
            <param name="file_input" value="MRSA0252.fna"/>
            <param name="min_cov" value="100"/>
            <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
        </test>

        <!-- Filetype test 7 - input a gbk -->
        <test>
            <param name="file_input" value="test.gbk"/>
            <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
        </test>