view alveo_get_item_data.xml @ 4:3a9f20428cff draft

planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty

<tool id="alveo_get_item_data" name="Get Alveo Data for Items" version="0.01" force_history_refresh="True">
    <description>Downloads files from the items in an Galaxy list of items</description>

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

    <command interpreter="python">
        alveo_get_item_data.py --api_key $api_key --item_list $item_list --patterns $patterns,$patternselect --output_path ItemListData
    </command>

    <inputs>
        <param name="api_key" type="data" format="txt" label="API Key" help="Your Alveo API key"/>
        <param name="item_list" type="data" format="tabular" label="Item List (table)" help=""/>

        <param name="patternselect" type="select" multiple="true" label="Predefined imports" display="checkboxes">
            <option value='*'>All Files</option>
            <option value='*speaker16.wav'>Austalk 16bit/16kHz Speaker Headset WAV (*speaker16.wav)</option>
            <option value='*plain.txt'>Plain text documents (*plain.txt)</option>
            <option value='*.txt'>All text documents (*.txt)</option>
            <option value=''>Other - enter pattern below</option>
        </param>

        <param name="patterns" type="text" label="File patterns to import"
               optional="true"
               help="One or more file patterns separated by commas eg. *.wav,*.txt"/>

        <param name="job_name" type="text" size="25"
               label="Supply a name for the output to remind you what it contains" value="Alveo Data"/>
    </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="item_list" value="hvd-sample-items.dat"/>
            <param name="patterns" value="*.TextGrid"/>
            <param name="patternselect" value=""/>
            <param name="output_path" value="test_out"/>
            <output_collection name="output1" type="list" count="5">
                    <element name="1_1308_2_22_023">
                        <assert_contents>
                            <has_text_matching expression="xmax = 1.020000"/>
                        </assert_contents>
                    </element>
            </output_collection>
        </test>
    </tests>

    <help>Downloads files from a local list of Alveo items. You can download all files or those matching
        a wildcard pattern (e.g. *.txt).  Results will be stored as a dataset collection in
        your history.</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>