Data generated by the external tool can be imported using a high throughput sequencing importer or processed by a post processing tool on the CLC Server. A general description of this is given in this section. For further details, please refer to section 12.7, which covers configuring Bowtie as an external application. There, two post processing tools are configured for the import of the results.
To configure a high throughput sequencing importer or post processing tool:
- Choose the option Output file from CL for the relevant parameter.
- 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.
- Click on the small triangle beside the High-throughtput sequencing import / Post processing heading to reveal that section.
- 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 12.4 for an example.
Figure 12.4: The parameters for high throughput sequencing importers and post processing tools are configured in a window like this. Here, the external application parameter "Name of copied sequence" has been clicked on next to "Selected files" to select it as input to the tool. Other parameters have been left with their default settings. As all the parameters show a locked symbol, none of them will be offered to the end user to view or change.
- 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.
- Configure any of the other parameters that you wish to. This includes:
- Changing the values of default fields. To edit fields that are locked by default, click on the symbol of the lock image to open the lock, then make changes.
- Choosing the parameters to be visible and editable by end users when they run the tool. A parameter with an unlocked symbol beside it will be shown to the end user and will be editable by them. Locked parameters will not be shown and cannot be changed by end users.
After configuration is complete, the text displayed in the General Configuration panel for the second drop down field of the relevant parameter will indicate which tool it has been linked to. 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 the relevant 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.