Specifying SMRT Pipe parameters

The --params option is the most important SMRT Pipe option, and is required for any sophisticated use. The option specifies an XML file that controls:

• The analysis modules to run.
• The order of execution.
• The parameters used by the modules.

The general structure of the settings XML file is as follows:

<?xml version="1.0"?>
<smrtpipeSettings>

<protocol>
...global parameters...
</protocol>

<module id="module_1">
...parameters...
</module>

<module id="module_2">
...parameters...
</module>

</smrtpipeSettings>