Mercurial > repos > melissacline > ucsc_xena_platform
annotate xenaAdmin.xml @ 13:be73a33f333b
Tweaking of ucsc data pages tool
| author | melissacline |
|---|---|
| date | Thu, 19 Mar 2015 14:08:11 -0700 |
| parents | ca4510434eda |
| children | 77f5d8cbac77 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="xenaAdmin" name="Xena Administration" version="0.0.2"> |
| 2 <description>Administer the Galaxy-embedded Xena: start, check status, stop, backup, restore</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0">installXena</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 #if $adminAction.actionType == "backup": | |
| 8 xena_backup.py ${adminAction.backupDir} $outfile | |
|
1
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
9 #else if $adminAction.actionType == "restore": |
|
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
10 xena_restore.py ${adminAction.restoreDir} $outfile |
|
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
11 #else if $adminAction.actionType == "delete": |
|
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
12 xena_delete.py ${adminAction.datasetId} $outfile |
| 0 | 13 #else: |
|
1
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
14 runXena.py ${adminAction.actionType} $outfile |
| 0 | 15 #end if |
| 16 </command> | |
| 17 <inputs> | |
| 18 <conditional name="adminAction"> | |
| 19 <param format="str" type="select" name = "actionType" label="Action"> | |
| 20 <option value="status">Check Status</option> | |
| 21 <option value="start">Start Xena</option> | |
| 22 <option value="stop">Stop Xena</option> | |
| 23 <option value="backup">Backup the Xena data to an external directory</option> | |
| 24 <option value="restore">Restore data to Xena from an external backup directory</option> | |
|
1
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
25 <option value="delete">Delete a dataset from the local Galaxy-embedded Xena</option> |
| 0 | 26 </param> |
| 27 <when value="backup"> | |
| 28 <param label="External Directory" type="text" name="backupDir" value="/tmp/xena_files"/> | |
| 29 </when> | |
| 30 <when value="restore"> | |
| 31 <param label="Backup Directory" type="text" name="restoreDir" value="/tmp/xena_files"/> | |
| 32 </when> | |
|
1
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
33 <when value="delete"> |
|
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
34 <param label="Dataset ID" type="text" name="datasetId"/> |
|
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
35 </when> |
| 0 | 36 <when value="status"/> |
| 37 <when value="start"/> | |
| 38 <when value="stop"/> | |
| 39 </conditional> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data format="txt" name="outfile"/> | |
| 43 </outputs> | |
| 44 <help> | |
| 45 | |
| 46 **Xena Administration** | |
| 47 | |
| 48 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. | |
| 49 | |
| 50 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. | |
|
1
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
51 |
|
ca4510434eda
Moved the xena delete functionality into xena admin
melissacline
parents:
0
diff
changeset
|
52 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. |
| 0 | 53 |
| 54 </help> | |
| 55 </tool> | |
| 56 | |
| 57 | |
| 58 |