Creating a metadata table directly in the Workbench

Metadata tables can be created from within the CLC Genomics Workbench. Generally, it is much easier to enter the metadata into an Excel file and either import that, as described in Importing metadata, or to use that file when launching a workflow in batch, and use the workflow results metadata file that is output, which is described in Workflow outputs and workflow result metadata tables.

To create a metadata table directly in the CLC Genomics Workbench, go to:

        File | New | Metadata Table (Image motiflist)

This opens a new metadata table with no columns and no rows. Importing metadata using the Metadata Table Editor requires that the table structure is defined first.

Defining the table structure

Click Setup Table at the bottom of the view (figure 11.6).

Image metadata_edit_columns
Figure 11.6: Dialog used to add columns to an empty Metadata Table.

To create a metadata table from scratch, use the "Add column right" or "Add column left" buttons (Image insert_column_after_16_n_p) to define the table structure with the amount of columns you will need, and edit the fields of each column as needed.

To import the table from a file, click on Setup Structure from File. In the dialog that appears (figure 11.7), you need to provide the following information:

Image metadata_import_columns
Figure 11.7: Creating a metadata table structure based on an external file.

For each column in the external file, a column will be created in the new metadata table. By default the type of these imported columns is "Text". You will see a reminder to set the column type for each column and to designate one of the columns as the key column.

Populating the table

Click on Manage Data button at the bottom of the view (figure 11.8).

Image metadata_edit_rows
Figure 11.8: Tool for managing the metadata itself. Notice the button labeled Import Rows from File.

The metadata table can then be populated by editing each column manually. Row information is added manually by clicking on the (Image insert_row_after_16_n_p) button and typing in the information for each column.

It is also possible to import information from an external file. In that case, the column names in the metadata table in the workbench will be matched with those in the external file to determine which values go into which cell. Only cell values in columns with an exact name match will be imported. If the file used contains columns not in the metadata table, the values in those columns will be ignored. Conversely, if the metadata table contains columns not present in the file, imported rows will have no values for those columns.

Click on Import Rows from File and select the external file of metadata. This brings up the window shown in figure 11.9.

Image metadata_import_rows
Figure 11.9: Tool to import rows into a Metadata Table.

When working with an existing metadata table and adding extra rows, it is generally recommended that a key column be designated first. If a key column is not present, then all rows in the file will be imported. With no key column designated, if any rows from that file were imported into the same metadata table earlier, a duplicate row will be created. With a key column, rows with a new, unique entry for that column are added to the table and existing rows with a key entry in the file will be updated, incorporating any changes present in the file. Duplicate rows will not be created.

The options presented in the Import Metadata Rows into Metadata Table are:

Click the button labeled Finish button when the necessary fields have been filled in.

The progress and status of the row import can be seen in the Processes tab of the Toolbox. Any errors resulting from an import that failed can be reviewed here. The most frequent errors are associated with selecting the wrong separator or encoding, or wrong date/time formats when importing rows from delimited text files.

Once the rows are imported, The metadata table can be saved.