view data_manager_build_ariba_database/data_manager/ariba_database_builder.xml.bk @ 3:6aabe4f367fd draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ariba commit 067b5a6a02d5f04c2155b45eed5df257a1360645-dirty

<?xml version="1.0"?>
<tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@">
    <description>database builder</description>
     <expand macro="requirements" />
    <version_command>ariba version | head head -n 1</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        #set $library_list = str($libraries).split(',')
        mkdir ariba-database && cd ariba-database &&
        #for $library in $library_list:
            #if str($library) != 'None':
                ariba getref $library _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv $library &&
            #end if
        #end for
        #for $fasta in $input_fasta:
            #if str($fasta) != 'None':
                ariba preparef --all_coding no $fasta $fasta    &&
            #end if
        #end for
        cd .. && 
        python '$__tool_directory__/ariba_data_base_builder.py' --db '${database_name}' --out '${out_file}'
    ]]>
    </command>
    <inputs>
        <param name="database_name" type="text" label="Name for this database" />
        <param name="libraries" type="select" multiple="true" label="Select partial library to download">
            <option value="card">CARD</option>
            <option value="resfinder">Resfinder</option>
            <option value="plasmidfinder">Plasmidfinder</option>
        </param>
        <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
    </help>
    <citations>
        <citation type="doi">110.1099/mgen.0.000131</citation>
    </citations>
</tool>