Mercurial > repos > melissacline > ucsc_xena_platform

annotate xenaGetDataset.xml @ 3:98b498545a52

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Fixed xena_delete to delete the files from the Xena files directory as well as from the database
author melissacline
date Wed, 14 Jan 2015 16:35:12 -0800
parents 8bb037f88ed2
children 066ae9df2d27
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1 <tool id="xenaGetDataset" description="Get a specified dataset and metadata from the Xena database" name="Get Data in Xena" version="0.0.2">
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2 <description>
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3 Retrieve a dataset from Xena
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.0">installXena</requirement>
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7 </requirements>
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8 <command interpreter="python">
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9 xenaGetDataset.py $dataHub $dataset $metadataFile $dataFile
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10 </command>
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11 <inputs>
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12 <param type="select" name="dataHub" label="Data Hub" optional="false">
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13 <option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
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14 </param>
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15 <param type="text" name="dataset" label="Dataset ID" optional="false"/>
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="metadataFile" label="${dataset}.json"/>
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19 <data format="tabular" name="dataFile" label="${dataset}" />
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20 </outputs>
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21 <help>
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22 Given the URL of a Xena dataset, download the data into a Galaxy dataset. Enter the URL of the dataset in the Dataset URL field. Xena dataset URLs 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.
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23 </help>
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24 </tool>