primer3_command_line.xml

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<primer3Doc version="1.0">
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An example Tag with all possible options:

<tag>
	<tagName></tagName>
	<description>
<![CDATA[<p> </p>]]>
	</description>
</tag>

	-->
<tag>
	<tagName>--about</tagName>
	<description>
<![CDATA[<p>With this argument Primer3 generates one line of output
indicating the release number and then exits. This allows scripts to 
query Primer3 for its version.</p>]]>
	</description>
</tag>

<tag>
	<tagName>--default_version=<i>n</i></tagName>
	<description>
<![CDATA[<p><i>n</i>=2 is the default, and directs primer3_core
to use the latest default values (the ones documented here).
<i>n</i>=1 directs primer3_core to use defaults from version
2.2.3 and before.
</p>]]>
	</description>
</tag>

<tag>
	<tagName>--format_output</tagName>
	<description>
<![CDATA[<p>This argument indicates that primer3_core should generate
user-oriented (rather than program-oriented) output.</p>]]>
	</description>
</tag>
<tag>
	<tagName>--strict_tags</tagName>
	<description>
<![CDATA[<p>This argument indicates that primer3_core should generate
a fatal error if there is any tag in the input that
it does not recognize.  This tag also applies to the settings file (see
documentation for the --p3_settings_file argument),
if any, but with limitations:  lines that do not begin with
PRIMER_ or P3_FILE_ID are always ignored in the settings file.</p>]]>
	</description>
</tag>
<tag>
	<tagName>--p3_settings_file=<i>file_path</i> </tagName>
	<description>
<![CDATA[<p>This argument specifies a settings file,
<i>file_path</i>. Primer3 reads the global 
("PRIMER_...") parameters from this file first. 
Tags appearing in the settings file override
default Primer3 settings. The values set in
the settings files can be also overridden 
by tags in the input file. See
Primer3 file documentation for details on the file 
format.  <strong>WARNING: the --strict_tags flag applies only to
tags beginning with the string "PRIMER_"; lines that do
not begin with the string "PRIMER_" are ignored.</strong></p>]]>
	</description>
</tag>
<tag>
	<tagName>--echo_settings_file</tagName>
	<description>
<![CDATA[<p>This argument indicates that primer3_core
should print the input tags specified
in the given settings file. If no settings file is
provided or if the --format_output option is given,
this argument will have no effect.</p>]]>
	</description>
</tag>
<tag>
	<tagName>--io_version=<i>n</i></tagName>
	<description>
<![CDATA[<p>This argument is provided for backward compatibility.
--io_version=4 <strong>is the only legal value and the default
</strong>.</p>]]>
	</description>
</tag>
<tag>
        <tagName>--output=<i>file_path</i></tagName>
        <description>
<![CDATA[<p>This argument specifies the file where the output
should be written. If omitted, stdout is used. </p>]]>
        </description>
</tag>
<tag>
        <tagName>--error=<i>file_path</i></tagName>
        <description>
<![CDATA[<p>This argument specifies the file where the error 
messages should be written. If omitted, stderr is used.</p>]]>
        </description>
</tag>
</primer3Doc>