<?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>