diff xenaGetDataset.xml @ 41:02b0824c7d60

Download data from any hub in the federated xena platform

--- a/xenaGetDataset.xml	Mon Jul 27 00:59:02 2015 -0700
+++ b/xenaGetDataset.xml	Mon Jul 27 10:05:22 2015 -0700
@@ -1,24 +1,37 @@
 <tool id="xenaGetDataset"  name="Get Data from Xena" version="0.0.2">
   <description>
-    Get a specified dataset and its associated metadata from the federated Xena platfrom
+    Download individual dataset from the federated Xena platfrom
   </description>
   <requirements>
     <requirement type="package" version="1.0">installXena</requirement>
   </requirements>
   <command interpreter="python">
-    xenaGetDataset.py $dataHub $dataset $metadataFile $dataFile
+    #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 $dataFile
+    #end if
   </command>
   <inputs>
-    <param type="select" name="dataHub" label="Data Hub" optional="false">
-      <option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
-    </param>
+    <conditional name="hub">
+      <param type="select" name="dataHub" label="Data Hub" optional="false">
+	<option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
+	<option value="datahub">Enter a different hub</option>
+      </param>
+      <when value ="https://genome-cancer.ucsc.edu/proj/public/xena"/>
+      <when value ="datahub">
+	<param type="text" name ="customDataHub" label="Hub url" optional="false"/>
+      </when>
+    </conditional>  
     <param type="text" name="dataset" label="Dataset ID" optional="false"/>
   </inputs>
   <outputs>
-    <data format="txt" name="metadataFile" label="${dataset}.json"/>
+    <!-- <data format="txt" name="metadataFile" label="${dataset}.json"/> -->
     <data format="tabular" name="dataFile" label="${dataset}" />
   </outputs>
   <help>
-    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.
+    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>