XMLparameters

###Introduction

The analysis is controlled by XML files containing the parameters for the analysis. These can be generated through the GUI under "Specify Analysis Parameters" or manually. For a list of parameters used for centromere finding, see Centromere Finder Parameters. A sample parameter file for centromere finding is in the downloads section. For other methods, consult their documentation or source code.

###Manual generation of XML parameter files

The general format of one of these xml files is:

<?xml version="1.0" ?>
<root>
<parameter></parameter>
.
.
.
<parameter></parameter>
</root>

where any number of parameters can be specified in between the <root></root> tags.

A parameter's name and value are specified using attributes in the parameter tag. There are three requirements: name, value, and type. The attribute displayname is optional, and can be used to add a more user-friendly name to display, for instance, in a gui for parameter selection. The name and value tags should have values in a double-quote delimited string. Type must be one of "boolean", "integer", "floating", or "string", and regardless of which is chosen, the value should be specified as a double-quoted string in the parameters file (for instance value="5" rather than value=5), and it will be converted later.

A complete parameter element looks like (for an example parameter):

<parameter name="pixelsize_nm" displayname="Pixel size, in nm" type="floating", value="80.0"></parameter>

You can also include between the parameter start and end tags a <description></description> element with plain text in between the description start and end tags, to provide a more verbose description of the parameter.

For a list of parameters used for centromere finding, see Centromere Finder Parameters. For other methods, consult their documentation or source code.

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