view alveo_get_item_list.xml @ 18:5e1b7d922ea3 draft default tip

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7

<tool id="alveo_get_item_list" name="Import Item List" version="1.0">
    <description>Retrieves Item URLs from an Alveo Item List</description>

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

    <command interpreter="python">
        alveo_get_item_list.py --api_key $api_key --item_list_url $item_list_url --output $output
    </command>

    <!--
        code file implements the dynamic_options below to fetch the users item
        lists from the Alveo API
    -->
    <code file="item_list_util.py" />

    <inputs>
        <param name="api_key" type="data" format="auth_token" label="API Key"
               help="Your Alveo API key (use Store Alveo API Key tool to create)"/>

        <param name="item_list_url" type="select"
               dynamic_options="ds_item_lists_options(api_key)"
               label="Alveo Item List"
               help="The Alveo Item List you wish to import (requires API Key)"/>

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

    <outputs>
        <data format="item_list" name="output" label="${job_name}"/>
    </outputs>

    <tests>
        <test>
            <param name="api_key" value="api-key.dat"/>
            <param name="item_list_url" value="https://app.alveo.edu.au/item_lists/180"/>
            <param name="job_name" value="test_output_180.dat"/>
            <output name="output" file="item_list_180.dat"/>
        </test>
    </tests>

    <help>Get the URLs of all of the items 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>