The first option you are presented with is the option to Rename the element. This is for example useful when you wish to discriminate several copies of the same tool in a workflow. The name of the element is also visible as part of the process description when the workflow is executed. Right click on the tool in the workflow and select "Rename" or click on the tool in the workflow and use the F2 key as a shortcut.
With the Remove option, elements can be removed from the workflow. The shortcut Alt + Shift + R removes all elements from the workflow.
You can also Configure the tool from the right click menu or alternatively it can be done by double-clicking the element. This will open a dialog with options for setting parameters, selecting reference data etc. An example is shown in figure 9.4.
Click through the dialogs using Next and press Finish when you are done. This will save the parameter settings that will then be applied when the workflow is executed.
You can also change the name of the parameter into something that fits the vocabulary of the users that are intended to execute the workflow. This is done by clicking the edit icon () and entering a new name.
Note that reference data are a bit special. In the example with the read mapper in figure 9.3, you have to define a reference genome. This is done by pointing to data in the Navigation Area. If you distribute the workflow and install it in a different setting where this data is not accessible, the installation procedure will involve defining the new reference data to use (e.g. the reference genome sequence for read mapping). This is explained in more detail in Installing a workflow in the Workbench.
In some workflows, many elements use the same reference data, and there is a quick way of configuring all these: right-click the empty space and choose Configure All References. This will show a dialog listing all reference data needed by the workflow.
The lock icons in the dialog are used for specifying whether the parameter should be locked and unlocked as described in Locking and unlocking parameters. Hereby it is possible to lock so the workflow runs with the same parameters like references(s) every time.
Once an element has been configured, the workflow element gets a darker color to make it easy to see which elements have been configured.
With Highlight Subsequent Path the path from Name of the tool that was clicked on and further downstream will be highlighted whereas all other elements will be grayed out (figure 9.5). The Remove Highlighting Subsequent Path reverts the highlighting to the normal workflow layout.
Instead of configuring the various tools individually, the Configuration Editor enable specification of all settings, references, masking parameters etc. through a single wizard window (figure 9.6). The Editor is accessed through the () icon located lower left corner.