A description of the value types that can be configured is given below. A tool tip providing a description of each type is also available by hovering the mouse cursor over it.
Some types allow a default value to be entered. This is indicated by the presence of an empty field beside it. Default values are displayed via the Workbench wizard and in the CLC Server Command Line Tools help. A default value specified this way will be used if the user does not change it, or in the case of the CLC Server Command Line Tools, when the user does not specify the parameter the value is associated with.
Another level of configuration is available for exporters, high throughput sequencing importers and post-processing tools, where the administrator can set default values and also choose if these should be visible and editable by end users. This is described in Configuring export from the CLC Server for an external application and High throughput sequencing importers and post processing tools respectively.
- Text - The end user can provide text that will be substituted into the command at runtime. A default value can be configured.
- Integer - The end user can provide a whole number that will be substituted into the command at runtime. A default value can be configured. If no value is set, then 0 is the default used.
- Double - The end user can provide a number that will be substituted into the command at runtime. A default value can be configured. If no value is set, then 0 is the default used.
- Boolean text - A checkbox is shown in the Workbench wizard interface. If the user checks the box, the given text will be substituted into the command at runtime. If the box is unchecked, this means that no value will be substituted.
- CSV enum - A drop down list is presented to a Workbench end user, from which they can choose a desired option. A corresponding value that will be substituted into the command at runtime. To configure this parameter type, enter a comma delimited list of the values to be substituted at runtime into the first box, and a comma delimited list of corresponding labels to display to end users in the second box. Each entry in a given list should be unique and the two lists should be of equal length.
For an example of this, please see Velvet integration on setting up Velvet as an external application.
- User-selected input data (CLC data location) - The end user should specify one or more input files from those stored on the CLC Server. The data selected will be exported from the CLC Server, so which exporter, and any additional parameter settings for that exporter, need to be configured. This is described in detail in section Configuring export from the CLC Server for an external application.
- User-selected files (Import/Export directory) - The end user should specify one or more input files from those stored in an Import/Export area on the CLC Server. These would typically not be .clc files Files can be configured so they are pre-selected for the end user. The end user can deselect pre-configured files when launching the external application via the Workbench.
- Output file from CL - This option specifies how the output of the external tool should be handled. This is described in detail in Handling the output of an external tool.
- File - The end user should specify an input file from their local machine. This would typically not be a .clc file
- Context substitute - The options are:
- CPU limit max cores The core limit defined for the server that executes the command will be substituted.
- Name of user The name of the user who launched the external application will be substituted.
- Boolean compound - This enables the creation of a checkbox. If checked, the end user is presented with another option as configured by the administrator. If not checked, the option associated with the checkbox is grayed out. Whether the box is checked or unchecked by default can be configured.