<?xml version=“1.0” encoding=“UTF-8”?> <bioml>

<note>This file is for all tandem parameters that we expose via command-line flags to the tandem_search.rb tool.  The command-line flags and their defaults always override the values in this file.</note>

<note>File Paths</note>
<note type="input" label="list path, taxonomy information">no default</note>
<note type="input" label="protein, taxon">no default</note>
<note type="input" label="spectrum, path">no default</note>
<note type="input" label="output, path">no default</note>

<note> DEFAULT PARAMETERS. One of the following;
        User supplied
        isb_default_input_native.xml
        gpm_default_input.xml
</note> 
<note type="input" label="list path, default parameters">no default</note>

<note> 
        REFINEMENT. Not supported via tandem_search.rb. 
        Put refinement params directly in a user defined defaults.xml
</note>
<note type="input" label="refine">no</note>

</bioml>