Mercurial > repos > melissacline > ucsc_xena_platform

annotate 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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066ae9df2d27 labeling descriptions edit
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1 <tool id="xenaGetDataset" name="Get Data from Xena" version="0.0.2">
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2 <description>
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3 Download individual dataset from the federated Xena platfrom
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.0">installXena</requirement>
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7 </requirements>
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8 <command interpreter="python">
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9 #if $hub.dataHub == "https://genome-cancer.ucsc.edu/proj/public/xena":
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10 xenaGetDataset.py $hub.dataHub $dataset $dataFile
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11 #elif $hub.customDataHub:
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12 getXenaData.py $hub.customDataHub $dataset $dataFile
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13 #else
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14 getXenaData.py $hub.dataHub $dataset $dataFile
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15 #end if
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16 </command>
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17 <inputs>
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18 <conditional name="hub">
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19 <param type="select" name="dataHub" label="Data Hub" optional="false">
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20 <option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
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21 <option value="datahub">Enter a different hub</option>
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22 </param>
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23 <when value ="https://genome-cancer.ucsc.edu/proj/public/xena"/>
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24 <when value ="datahub">
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25 <param type="text" name ="customDataHub" label="Hub url" optional="false"/>
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26 </when>
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27 </conditional>
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28 <param type="text" name="dataset" label="Dataset ID" optional="false"/>
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29 </inputs>
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30 <outputs>
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31 <!-- <data format="txt" name="metadataFile" label="${dataset}.json"/> -->
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32 <data format="tabular" name="dataFile" label="${dataset}" />
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33 </outputs>
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34 <help>
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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.
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36 </help>
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37 </tool>