Mercurial > repos > melissacline > ucsc_xena_platform
annotate xenaGetDataset.xml @ 39:066ae9df2d27
labeling descriptions edit
| author | jingchunzhu <jingchunzhu@gmail.com> |
|---|---|
| date | Mon, 27 Jul 2015 00:46:53 -0700 |
| parents | 8bb037f88ed2 |
| children | fd24e220f240 |
| rev | line source |
|---|---|
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066ae9df2d27
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jingchunzhu <jingchunzhu@gmail.com>
parents:
0
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changeset
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1 <tool id="xenaGetDataset" name="Get Data from Xena" version="0.0.2"> |
| 0 | 2 <description> |
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066ae9df2d27
labeling descriptions edit
jingchunzhu <jingchunzhu@gmail.com>
parents:
0
diff
changeset
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3 Get a specified dataset and its associated metadata from the Xena database |
| 0 | 4 </description> |
| 5 <requirements> | |
| 6 <requirement type="package" version="1.0">installXena</requirement> | |
| 7 </requirements> | |
| 8 <command interpreter="python"> | |
| 9 xenaGetDataset.py $dataHub $dataset $metadataFile $dataFile | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param type="select" name="dataHub" label="Data Hub" optional="false"> | |
| 13 <option value="https://genome-cancer.ucsc.edu/proj/public/xena"/> | |
| 14 </param> | |
| 15 <param type="text" name="dataset" label="Dataset ID" optional="false"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="txt" name="metadataFile" label="${dataset}.json"/> | |
| 19 <data format="tabular" name="dataFile" label="${dataset}" /> | |
| 20 </outputs> | |
| 21 <help> | |
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39
066ae9df2d27
labeling descriptions edit
jingchunzhu <jingchunzhu@gmail.com>
parents:
0
diff
changeset
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22 Given the data hub name and the dataset id, download the data into a Galaxy dataset. Xena dataset id can be obtained through the Explore Data in Xena tool. The accompanying metadata will be downloaded automatically along with the data, and will be stored in a second Galaxy dataset. |
| 0 | 23 </help> |
| 24 </tool> |