comparison abricate.xml @ 5:f9bf6a8d8547 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit c272325e121abb0582d2a50759ee04b43f327d4d"

4:78c75f134c16

    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />

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

5:f9bf6a8d8547

    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />

    <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