Mercurial > repos > melissacline > ucsc_xena_platform
changeset 1:ca4510434eda
Moved the xena delete functionality into xena admin
| author | melissacline |
|---|---|
| date | Wed, 14 Jan 2015 12:47:23 -0800 |
| parents | 8bb037f88ed2 |
| children | 6eeb3ca663fb |
| files | xenaAdmin.xml xena_delete.xml xena_utils.pyc |
| diffstat | 3 files changed, 11 insertions(+), 22 deletions(-) [+] |
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--- a/xenaAdmin.xml Tue Jan 13 23:37:23 2015 -0500 +++ b/xenaAdmin.xml Wed Jan 14 12:47:23 2015 -0800 @@ -6,12 +6,12 @@ <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: - #if $adminAction.actionType == "restore": - xena_restore.py ${adminAction.restoreDir} $outfile - #else: - runXena.py ${adminAction.actionType} $outfile - #end if + runXena.py ${adminAction.actionType} $outfile #end if </command> <inputs> @@ -22,6 +22,7 @@ <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"/> @@ -29,6 +30,9 @@ <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"/> @@ -44,6 +48,8 @@ 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>
--- a/xena_delete.xml Tue Jan 13 23:37:23 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -<tool id="xena_delete" description="Delete a dataset from the local Galaxy-embedded Xena" name="Delete Xena Dataset" version="0.0.1"> - <description> - Given the name of a dataset, delete it from the local Xena-embedded Galaxy. - </description> - <command interpreter="python"> - xena_delete.py $dataset $outfile - </command> - <inputs> - <param name="dataset" type="text" label="Dataset Name"/> - </inputs> - <outputs> - <data name="outfile" format="txt"/> - </outputs> - <help> - This tool will delete a dataset from the local Galaxy-embedded Xena database, given the name of the dataset. The names of the datasets can be seen through the Xena Data Hub tool, by selecting the local Galaxy-embedded Xena as the hub and viewing the datasets contained in that hub. This tool works only for the local Xena-embedded Galaxy. - </help> -</tool>