view xenaAdmin.xml @ 4:1707e82d55bc

Tweaking the parameter labels for the xena import tool

<tool id="xenaAdmin" name="Xena Administration" version="0.0.2">
  <description>Administer the Galaxy-embedded Xena: start, check status, stop, backup, restore</description>
 <requirements>
   <requirement type="package" version="1.0">installXena</requirement>
 </requirements>
  <command interpreter="python">
    #if $adminAction.actionType == "backup":
        xena_backup.py ${adminAction.backupDir} $outfile
    #else if $adminAction.actionType == "restore":
	xena_restore.py ${adminAction.restoreDir} $outfile
    #else if $adminAction.actionType == "delete":
	xena_delete.py ${adminAction.datasetId} $outfile
    #else:
        runXena.py ${adminAction.actionType} $outfile
    #end if
  </command>
  <inputs>
    <conditional name="adminAction">
      <param format="str" type="select" name = "actionType" label="Action">
	<option value="status">Check Status</option>
	<option value="start">Start Xena</option>
	<option value="stop">Stop Xena</option>
	<option value="backup">Backup the Xena data to an external directory</option>
	<option value="restore">Restore data to Xena from an external backup directory</option>
	<option value="delete">Delete a dataset from the local Galaxy-embedded Xena</option>
      </param>
      <when value="backup">
	<param label="External Directory" type="text" name="backupDir" value="/tmp/xena_files"/>
      </when>
      <when value="restore">
	<param label="Backup Directory" type="text" name="restoreDir" value="/tmp/xena_files"/>
      </when>
      <when value="delete">
	<param label="Dataset ID" type="text" name="datasetId"/>
      </when>
      <when value="status"/>
      <when value="start"/>
      <when value="stop"/>
    </conditional>
  </inputs>
  <outputs>
    <data format="txt" name="outfile"/>
  </outputs>
 <help>

**Xena Administration**      

Administer the Galaxy-embedded Xena by starting it, stopping it or checking its status.  If you start Xena, or if you check the status while Xena is running, the output will indicate a URL for the Xena server that you can enter in the Xena Data Hub tool.  After you add a new data hub with this URL, and select it, you will be able to see the data from this Xena in the Xena browser.

With this tool, you can also  backup the data from your Galaxy-embedded Xena to an external directory on the same computer, and can restore data from a previous backup into the Xena database.  If you wish to restore data, Xena must be running first.

Finally, you can use this tool to remove a dataset from the Galaxy-embedded local Xena.  Simply indicate the dataset by Dataset ID, which you will find under the Xena Data Pages.
   
  </help>
</tool>