view alveo_get_primary_text.xml @ 4:3a9f20428cff draft

planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty

<tool id="alveo_get_primary_text" name="Get Text from Alveo" version="0.01" force_history_refresh="True">
    <description>Downloads primary text from the items in an Alveo Item List</description>

    <requirements>
        <requirement type="package" version="0.6">pyalveo</requirement>
    </requirements>

    <command interpreter="python">
        alveo_get_primary_text.py --api_key $api_key --item_list_url $item_list_url --output_path ItemListData
    </command>

    <inputs>
        <param name="api_key" type="data" format="txt" label="API Key" help="Your Alveo API key"/>
        <param name="import_list" type="data" format="tabular" label="Imported Alveo Item List" help=""/>

        <param name="item_list_url" type="select" label="Alveo Item List" help="The Alveo Item List you wish to import">
            <options from_dataset="import_list">
                <column name="name" index="0"/>
                <column name="value" index="1"/>
            </options>
        </param>

        <param name="job_name" type="text" size="25"
               label="Supply a name for the outputs to remind you what they contain" value="Item List downloaded from Alveo"/>
    </inputs>

    <outputs>
        <collection type="list" label="$job_name" name="output1">
            <discover_datasets pattern="(?P&lt;designation&gt;[^_]+)_(?P&lt;ext&gt;.+)" directory="ItemListData"/>
        </collection>
    </outputs>

    <tests>
        <test>
            <param name="api_key" value="api-key.dat"/>
            <param name="import_list" value="item-lists.dat"/>
            <param name="item_list_url" value="https://app.alveo.edu.au/item_lists/180"/>
            <param name="output_path" value="test_out"/>
            <output_collection name="output1" type="list" count="6">
                    <element name="GCSAusE02">
                        <assert_contents>
                            <has_text_matching expression="background noises"/>
                        </assert_contents>
                    </element>
            </output_collection>
        </test>
        <test>
            <param name="api_key" value="api-key.dat"/>
            <param name="import_list" value="item-lists.dat"/>
            <param name="item_list_url" value="https://app.alveo.edu.au/item_lists/52"/>
            <param name="output_path" value="test_out"/>
            <output_collection name="output1" type="list" count="0">
            </output_collection>
        </test>
    </tests>

    <help>Downloads the primary text for each item from an Alveo Item List</help>
    <citations>
        <citation type='bibtex'>
            @article{cassidy2014alveo,
              title={The alveo virtual laboratory: a web based repository API},
              author={Cassidy, Steve and Estival, Dominique and Jones, Tim and Sefton, Peter and Burnham, Denis and Burghold, Jared and others},
              year={2014},
              publisher={Reykjavik, Iceland: European Language Resources Association}
            }
        </citation>
    </citations>
</tool>