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comparison xenaGetDataset.xml @ 41:02b0824c7d60

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Download data from any hub in the federated xena platform
author jingchunzhu <jingchunzhu@gmail.com>
date Mon, 27 Jul 2015 10:05:22 -0700
parents fd24e220f240
children 78d6e6772e30
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40:fd24e220f240 41:02b0824c7d60
1 <tool id="xenaGetDataset" name="Get Data from Xena" version="0.0.2"> 1 <tool id="xenaGetDataset" name="Get Data from Xena" version="0.0.2">
2 <description> 2 <description>
3 Get a specified dataset and its associated metadata from the federated Xena platfrom 3 Download individual dataset from the federated Xena platfrom
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.0">installXena</requirement> 6 <requirement type="package" version="1.0">installXena</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python"> 8 <command interpreter="python">
9 xenaGetDataset.py $dataHub $dataset $metadataFile $dataFile 9 #if $hub.dataHub == "https://genome-cancer.ucsc.edu/proj/public/xena":
10 xenaGetDataset.py $hub.dataHub $dataset $dataFile
11 #elif $hub.customDataHub:
12 getXenaData.py $hub.customDataHub $dataset $dataFile
13 #else
14 getXenaData.py $hub.dataHub $dataset $dataFile
15 #end if
10 </command> 16 </command>
11 <inputs> 17 <inputs>
12 <param type="select" name="dataHub" label="Data Hub" optional="false"> 18 <conditional name="hub">
13 <option value="https://genome-cancer.ucsc.edu/proj/public/xena"/> 19 <param type="select" name="dataHub" label="Data Hub" optional="false">
14 </param> 20 <option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
21 <option value="datahub">Enter a different hub</option>
22 </param>
23 <when value ="https://genome-cancer.ucsc.edu/proj/public/xena"/>
24 <when value ="datahub">
25 <param type="text" name ="customDataHub" label="Hub url" optional="false"/>
26 </when>
27 </conditional>
15 <param type="text" name="dataset" label="Dataset ID" optional="false"/> 28 <param type="text" name="dataset" label="Dataset ID" optional="false"/>
16 </inputs> 29 </inputs>
17 <outputs> 30 <outputs>
18 <data format="txt" name="metadataFile" label="${dataset}.json"/> 31 <!-- <data format="txt" name="metadataFile" label="${dataset}.json"/> -->
19 <data format="tabular" name="dataFile" label="${dataset}" /> 32 <data format="tabular" name="dataFile" label="${dataset}" />
20 </outputs> 33 </outputs>
21 <help> 34 <help>
22 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. 35 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.
23 </help> 36 </help>
24 </tool> 37 </tool>