view xenaGetDataset.xml @ 33:7ceb967147c3

start xena with no gui add library files

<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>