view data_manager_build_ariba_database/data_manager/ariba_database_builder.xml @ 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[
        #if str($library.lib_type) == "curated"
            #set $library_list = str($library.curated).split(',')
            #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
        #end if
        
        #if str($library.lib_type) == "fasta"
            #if str($library).fasta != 'None':
                ariba prepareref --all_coding '$coding' -f '$library.fasta' '$library.db_name'
            #end if
        #end if

        python '$__tool_directory__/ariba_data_base_builder.py'  --out '${out_file}'
    ]]>
    </command>
     <inputs>
        <conditional name="library">
        <param name="lib_type" type="select" label="Input reads type or collection" help="Select a curated database or a fasta from the history">
                <option value="curated" selected="true">Curated Database</option>
                <option value="fasta">A fasta file</option>
        </param>
        <when value="curated">
        <param name="curated" 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>
            <option value="megares">Megares</option>
            <option value="argannot">Argannot</option>
            <option value="vfdb_core">vfdb_core</option>
            <option value="vfdb_full">vfdb_full</option>
            <option value="virulencefinder">virulencefinder</option>
        </param>
        </when>
         <when value="fasta">
            <param name="fasta" type="data" format="fasta" optional="false" />
            <param name="db_name" type="text" label="DB name" help = "The DB name should include no space and special characters" />
            <param name="coding" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="Coding sequence?" />
         </when>
         </conditional>
    </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>