Data generated by the external tool can be imported using a high throughput sequencing importer or processed after import by a post processing tool on the CLC Server. To configure a high throughput sequencing importer or post processing tool:
- Choose the option Output file from CL for a parameter value in the General configuration area under the External command tab.
- Choose the option "No standard import or map to high throughput sequencing importer". Despite the name, this will also allow connections to be made to post processing tools.
- Open the High-throughtput sequencing import / Post processing tab.
- Click on the Add new button.
- Select the high throughput sequencing import or post processing tool of interest from the list.
- Click on the button below the list called Edit and map parameters.... This button appears when a tool is selected.
A new window showing all the parameters for that tool will appear. See figure 13.7 for an example.
- Select the relevant external application parameter to be used as input to the tool by clicking on it in the list.
For high throughput sequencing tools, the input parameter is usually called "Selected files". For post processing tools, the name of the input field varies, but the word "(input)" is usually present by that parameter name.
Figure 13.7: Clicking on the "Edit and map parameters..." button opens a window for configuring the selected tool. Here, the parameter "Copied sequences" has been selected by clicking on it, thereby specifying that the file associated with that parameter should be used as input to the tool. All the parameters here have a locked symbol beside them, so none of them will be editable or shown to end users.
- Configure any of the other parameters that you wish to, for example:
- Change the parameter values. To edit fields that are locked by default, click on the symbol of the lock image to open the lock, then make changes.
- Unlock parameters that should be visible and editable by end users by clicking on the lock symbol.
After configuration changes are saved, text in the General Configuration panel will be updated, making it clear which tool has was selected for use with a given command parameter. For example, if the post processing tool: "Import SAM/BAM Mapping Files" was configured and the relevant output mapped to it, the text in the General configuration area for that output would show: "Linked with Import SAM/BAM Mapping Files" in the second field.
If you change your mind about linking to a high throughput sequencing importer or post processing tool from an external application parameter, you must remove the connection between the two. This would usually be done by deleting the relevant configuration in the High-throughput sequencing import / Post processing area.