view alveo_get_primary_text.xml @ 17:b69f6d41d17c draft

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit f2432aaedd36ae7662873623d8861d0982dffdd2-dirty

<tool id="alveo_get_primary_text" name="Get Text from Alveo" version="1.0">
    <description>Downloads primary text from the items in an Alveo Item List</description>

    <requirements>
        <requirement type="package" version="1.0.5">pyalveo</requirement>
    </requirements>

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

    <inputs>
        <param name="api_key" type="data" format="auth_token" label="API Key" help="Your Alveo API key"/>
        <param name="item_list" type="data" format="item_list" label="Item List" help=""/>
    </inputs>

    <outputs>
        <collection type="list" label="$item_list Texts" 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="item_list" value="item_list_180.dat"/>
            <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="item_list" value="item_list_52.dat"/>
            <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>