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>

• The protocol element allows setting global parameters that could possibly be used by all modules.
• Each module element defines an analysis module to run.
• The order of the module elements defines the order in which the modules execute.

SMRT Portal protocol templates are located in: $SEYMOUR_HOME/common/protocols/.

SMRT Pipe modules are located in: $SEYMOUR_HOME/analysis/lib/pythonx.x/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/modules/.

You specify parameters by entering a key-value pair in a param element.

• The name of the key is in the name attribute of the param element.
• The value of the key is contained in a nested value element.

For example, to set the parameter named reference, you specify:

<param name="reference">
  <value>/share/references/repository/celegans</value>
</param>

Note: To reference a parameter value in other parameters, use the notation ${variable} when specifying a value. For example, to reference a global parameter named home, use it in other parameters as ${home}. SMRT Pipe supports arbitrary parameters in the settings XML file, so the use of temporary variables like this can help readability and maintainability.

Following is a complete example of a settings file for running filtering, mapping, and consensus steps against the E coli reference genome:

<?xml version="1.0" encoding="utf-8"?>
<smrtpipeSettings>
 <protocol>
  <param name="reference">
   <value>/share/references/repository/ecoli</value>
  </param>
 </protocol>

 <module name="P_Filter">
  <param name="minLength">
    <value>50</value>
  </param>
  <param name="readScore">
    <value>0.75</value>
  </param>
 </module>

 <module name="P_FilterReports" />

 <module name="P_Mapping">
  <param name="align_opts" hidden="true">
   <value>--minAccuracy=0.75 --minLength=50 -x </value>
  </param>
 </module>

 <module name="P_MappingReports" />
 <module name="P_Consensus" />
 <module name="P_ConsensusReports" />

</smrtpipeSettings>