Command line tools that are available on a machine or set of machines can be described in an use cases XML format, and then be imported to the Service Panel for drag-and-drop pre-configured Tool services into the workflow.
Known tool descriptions:
- http://taverna.nordugrid.org/sharedRepository/xml.php - tools available on NorduGrid ARC. See also the listed use cases
The use cases XML is a list of known
<program> with a
name="" and a
<group> can be used to organize the listing tree in Taverna. Multiple
output files can be specified. Example:
Importing a set of tool descriptions
- Click Import new services button in the Service Panel.
- Select Tool service...
- In a dialog that pops up, enter the URL of the tool description registry you have obtained from the service provider and click Add.
A pop up dialog will appear for you to enter the URL of the tool registry.
After you have imported a set of tool descriptions Service Panel, it will appear somewhere under your Available Services.
To locate a particular quicker, you may want to use the Filter at the top of the Service Panel.
You can now add an individual tool service to your workflow by drag and dropping them from the Service Panel to the Workflow Diagram.
When you add a tool from the registry into your workflow, the tool description is copied. This means that it is not automatically synchronized with later changes of the tool description in the registry.
Configuring a Tool Service
When you have included a tool service described in a registry into your workflow, you can choose to reconfigure it (e.g. to modify the command line parameters).
You can change where the tool will run under the Location tab (e.g. to an SSH server).
Under the Edit tab, you can use the check that the Update tool description button to check that the tool description you have in your workflow is up-to-date with that in the registry. You can also change the tool description by clicking the Edit tool description button. This allows you access to all the tool configuration options.
Currently tools described in a registry can have more capabilities than those exposed in the interface of Taverna Workbench. For this reason, some tool descriptions from a registry do not allow you to edit the tool description.