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view xenaGetDataset.xml @ 30:77f5d8cbac77

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add functionality to check the version of the current running xena server on the galaxy system
author Jing Zhu <jzhu@soe.ucsc.edu>
date Mon, 20 Jul 2015 13:31:33 -0700
parents 8bb037f88ed2
children 066ae9df2d27
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<tool id="xenaGetDataset" description="Get a specified dataset and metadata from the Xena database" name="Get Data in Xena" version="0.0.2">
  <description>
    Retrieve a dataset from Xena
  </description>
  <requirements>
    <requirement type="package" version="1.0">installXena</requirement>
  </requirements>
  <command interpreter="python">
    xenaGetDataset.py $dataHub $dataset $metadataFile $dataFile
  </command>
  <inputs>
    <param type="select" name="dataHub" label="Data Hub" optional="false">
      <option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
    </param>
    <param type="text" name="dataset" label="Dataset ID" optional="false"/>
  </inputs>
  <outputs>
    <data format="txt" name="metadataFile" label="${dataset}.json"/>
    <data format="tabular" name="dataFile" label="${dataset}" />
  </outputs>
  <help>
    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.
  </help>
</tool>