Mercurial > repos > melissacline > ucsc_xena_platform

view xenaGetDataset.xml @ 43:78d6e6772e30

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author jingchunzhu <jingchunzhu@gmail.com>
date Mon, 27 Jul 2015 12:21:55 -0700
parents 02b0824c7d60
children cdba6c63dce5
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<tool id="xenaGetDataset"  name="Get Data from Xena" version="0.0.2">
  <description>
    Download individual dataset from the federated Xena platfrom
  </description>
  <requirements>
    <requirement type="package" version="1.0">installXena</requirement>
  </requirements>
  <command interpreter="python">
    #if $hub.dataHub == "https://genome-cancer.ucsc.edu/proj/public/xena":
        xenaGetDataset.py $hub.dataHub $dataset $dataFile
    #elif $hub.customDataHub:
        getXenaData.py $hub.customDataHub $dataset $dataFile
    #else
        getXenaData.py $hub.dataHub $dataset $dataFile
    #end if
  </command>
  <inputs>
    <conditional name="hub">
      <param type="select" name="dataHub" label="Data Hub" optional="false">
	<option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
	<option value="datahub">Enter a different hub</option>
      </param>
      <when value ="https://genome-cancer.ucsc.edu/proj/public/xena"/>
      <when value ="datahub">
	<param type="text" name ="customDataHub" label="Hub url" optional="false"/>
      </when>
    </conditional>  
    <param type="text" name="dataset" label="Dataset ID" optional="false"/>
  </inputs>
  <outputs>
    <!-- <data format="txt" name="metadataFile" label="${dataset}.json"/> -->
    <data format="txt" name="dataFile" label="${dataset}" />
  </outputs>
  <help>
    Given the data hub name and the dataset id, download the dataset into this Galaxy. Xena dataset id can be obtained through the Explore Data in Xena tool.
  </help>
</tool>