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

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

<tool id="alveo_get_item_data" name="Get Alveo Data" version="1.0">
    <description>Downloads files from the items in an item list</description>

    <requirements>
        <requirement type="package" version="1.0.5">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="auth_token"
               label="API Key" help="Your Alveo API key (use Store Alveo API Key to get this)"/>

        <param name="item_list" type="data"
               format="item_list" label="Item List (table)"
               help="Item list (use Import Item List tool to get this)"/>

        <param name="patternselect" type="select" multiple="false"
               label="Predefined imports" display="radio">
            <option value='PRIMARYTEXT'>Primary text of each item (best for text analysis)</option>
            <option value='*speaker16.wav'>Austalk 16bit/16kHz Speaker Headset WAV (*speaker16.wav)</option>
            <option value='*.txt'>All text documents (*.txt)</option>
            <option value='*'>All files attached to item (*)</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>
        <test>
            <param name="api_key" value="api-key.dat"/>
            <param name="item_list" value="item_list_189.dat"/>
            <param name="patterns" value=""/>
            <param name="patternselect" value="PRIMARYTEXT"/>
            <param name="output_path" value="test_out"/>
            <output_collection name="output1" type="list" count="5">
                <element name="S1A-001-plain">
                    <assert_contents>
                        <has_text_matching expression="forename2 starts on the dot"/>
                    </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>