view data_manager/FROGS_data_manager.xml @ 11:0cc5f020640e draft default tip

planemo upload commit b0ebe74a020dcb21b79d8d39e7b6a2f6533b2fc4-dirty

<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.28.1" tool_type="manage_data">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        python $__tool_directory__/FROGS_data_manager.py
            --database="$database.database"
            #if $database.database=="frogs_db_data"
                --all_dbs="$database.db_type.db"
                #if $database.db_type.db=="false"
                    --date="$database.db_type.date"
                    --amplicons="$database.db_type.amplicons"
                    --bases="$database.db_type.bases"
                    --filters="$database.db_type.filters"
                #end if
                --only_last_versions="$database.only_last_versions"
            #end if 
            --tool_data="$__tool_data_path__"
            --output "$output"
    ]]></command>
    <inputs>
        <conditional name="database">
            <param name="database" type="select" label="Please select a database to update">
                <option value="frogs_db_data">FROGS database (FROGS Affiliation OTU)</option>
                <option value="HVL_db_data">HVL database (FROGS Affiliation postprocess)</option>
            </param>
            <when value="frogs_db_data">
                <conditional name="db_type">
                    <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/>
                    <when value="true"/>
                    <when value="false">
                        <param name="date" value="0" type="text"  label="Only more recent database than this date will be downloaded" help="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">
                            <validator type="regex" message="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">0|[1-2]{1}[0-9]{3}[0-1]{1}[0-9]{1}([0-2]{1}[0-9]{1}|3[0-1]{1})</validator>
                        </param>
                        <param name="amplicons" type="text" label='Select database to download by amplicons, put an amplicons list separated by "," ' help='example: "COI,ITS,16S" or "23S"'/>
                        <param name="bases" type="text" label='Select database to download by base, put a bases list separated by "," ' help='example: "SILVA,PR2,MIDAS" or "BOLD"'/>
                        <param name="filters" type="text" label='Select database to download by filters, put a filters list separated by "," ' help='example: "Pintail100,Fungi"'/>
                    </when>
                </conditional>
                <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of each database"/>
            </when>
            <when value="HVL_db_data"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="data_manager_json"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>