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annotate alveo_data_importer.xml @ 14:a38315ecf593 draft

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planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
author stevecassidy
date Wed, 01 Nov 2017 01:18:15 -0400
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children fd22df0c6d9b
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a38315ecf593 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
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1 <tool id="alveo_data_importer" name="Get Item URLs for Item List + API Key" version="0.01">
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2 <description>Stores API Key and Retrieves Item URLs from an Alveo Item List
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3 Version called directly from the Alveo web application
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4 </description>
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6 <requirements>
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7 <requirement type="package" version="0.7">pyalveo</requirement>
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8 </requirements>
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10 <command interpreter="python">
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11 alveo_data_importer.py --api_key $api_key --item_list_url $item_list --outputkey $outputkey --output $output
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12 </command>
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14 <inputs>
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15 <param name="api_key" type="text" size="30" label="API Key" help="Your Alveo API key"/>
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16 <param name="item_list" type="text" label="Alveo Item List URL" help="The Alveo Item List you wish to import"/>
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17 <param name="job_name" type="text" size="25"
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18 label="Supply a name for the outputs to remind you what they contain" value="Item List"/>
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19 </inputs>
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21 <outputs>
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22 <data format="auth_token" name="outputkey" label="Alveo API key" />
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23 <data format="item_list" name="output" label="${job_name}"/>
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24 </outputs>
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26 <tests>
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27 <test>
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28 <!-- expect this to fail unless you enter a valid API key here and copy it to
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29 the result file -->
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30 <param name="api_key" value="your api key here" />
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32 <param name="import_list" value="item-lists.dat"/>
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33 <param name="item_list_url" value="https://app.alveo.edu.au/item_lists/180"/>
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34 <param name="job_name" value="test_output_180.dat"/>
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35 <output name="outputkey" file="api-key.dat" compare="contains" />
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36 <output name="output" file="item_list_180.dat"/>
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37 </test>
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38 </tests>
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39
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40 <help>Store an API Key and get the URLs of all of the items from an Alveo item list.
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41 This is a combination of the "Store Alveo API Key" and "Get Item URLs for Item List"
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42 tools written so that it can be called directly from the Alveo web application
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43 item list page.</help>
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44 <citations>
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45 <citation type='bibtex'>
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46 @article{cassidy2014alveo,
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47 title={The {Alveo Virtual Laboratory}: a web based repository API},
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48 author={Cassidy, Steve and Estival, Dominique and Jones, Tim and Sefton, Peter and Burnham, Denis and Burghold, Jared and others},
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49 year={2014},
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50 publisher={Reykjavik, Iceland: European Language Resources Association}
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51 }
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52 </citation>
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53 </citations>
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54 </tool>