view data_manager/data_manager_manual.xml @ 10:ac682ae1c557 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616

<tool id="data_manager_manual" name="Manual Data Manager" version="0.0.3" tool_type="manage_data" profile="19.01">
    <options sanitize="False" />
    <description>Entry Builder</description>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/data_manager_manual.py'
        '${out_file}'
        --galaxy_data_manager_data_path '${__app__.config.galaxy_data_manager_data_path}'
    ]]></command>
    <inputs>
        <repeat name="data_tables" title="Data Table to define" min="1">
            <param name="data_table_name" type="select" multiple="False" optional="False" label="Choose Desired Data Table"
                dynamic_options="galaxy_code_get_available_data_tables( __trans__ )" refresh_on_change="True"/>
            <repeat name="columns" title="Table Columns" min="1">
                <param name="data_table_column_name" type="select" multiple="False" optional="False" label="Column Name"
                    dynamic_options="galaxy_code_get_available_data_table_columns( __trans__, data_table_name )" />
                <!-- <param name="data_table_column_name" type="text" label="Column Name"/> -->
                <param name="data_table_column_value" type="text" label="Value to use for data table column"/>
                <conditional name="is_path">
                    <param name="is_path_selector" type="select" label="Value is a path">
                        <option value="yes">Yes</option>
                        <option value="no" selected="True">No</option>
                    </param>
                    <when value="yes">
                        <param name="abspath" type="boolean" label="Apply abspath" checked="True" truevalue="abspath" falsevalue="" />
                    </when>
                    <when value="no"/>
                </conditional>
            </repeat>
        </repeat>
        <repeat name="directory_content" title="Directory Content">
            <param name="subdir" type="text" label="Place in Subdirectory" value=""/>
            <conditional name="file_source">
                <param name="file_source_selector" type="select" label="File Content Source">
                    <option value="history">History Item</option>
                    <option value="URL" selected="True">URL</option>
                </param>
                <when value="history">
                    <param name="file_history" type="data" multiple="false" optional="false" format="data" label="File from history" />
                </when>
                <when value="URL">
                    <param name="file_URL" type="text" label="Fetch from URL" value=""/>
                </when>
            </conditional>
            <conditional name="file_action">
                <param name="file_action_selector" type="select" label="File Actions">
                    <option value="unpack">Extract Archive</option>
                    <option value="None" selected="True">None</option>
                </param>
                <when value="None">
                    <param name="filename_override" type="text" label="Override with Filename" value=""/>
                </when>
                <when value="unpack">
                </when>
            </conditional>
        </repeat>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <repeat name="data_tables">
                <param name="data_table_name" value="__dbkeys__"/>
                <repeat name="columns">
                    <param name="data_table_column_name" value="value"/>
                    <param name="data_table_column_value" value="dm6"/>
                </repeat>
                <repeat name="columns">
                    <param name="data_table_column_name" value="name"/>
                    <param name="data_table_column_value" value="Drosophila melanogaster genome release 6"/>
                </repeat>
                <repeat name="columns">
                    <param name="data_table_column_name" value="len_path"/>
                    <param name="data_table_column_value" value="dm6.len"/>
                </repeat>
            </repeat>
            <output name="out_file" file="dm6.data_manager_json"/>
        </test>
    </tests>
    <help>
**What it does**

This tool allows manually specifying data table entries and optionally providing filesystem contents.

    </help>
    <code file="data_manager_manual.py" />
</tool>