<?xml version="1.0" encoding="UTF-8"?>
<bioml xmlns:GAML="http://www.bioml.com/gaml/" label="example api document">
    <group label="input parameters" type="parameters">
        <note type="input" label="output, histogram column width">30</note>
        <note type="input" label="output, histograms">yes</note>
        <note type="input" label="output, maximum valid expectation value">0.1</note>
        <note type="input" label="output, one sequence copy">yes</note>
        <note type="input" label="output, parameters">yes</note>
        <note type="input" label="output, path hashing">no</note>
        <note type="input" label="output, performance">yes</note>
        <note type="input" label="output, proteins">yes</note>
        <note type="input" label="output, mzid">yes</note>
        <note type="input" label="output, results">all</note>
        <note type="input" label="output, sequences">yes</note>
        <note type="input" label="output, sort results by">spectrum</note>
        <note type="input" label="output, spectra">yes</note>
        <note type="input" label="output, xsl path">tandem-style.xsl</note>
        <note type="input" label="protein, C-terminal residue modification mass">0.0</note>
        <note type="input" label="protein, N-terminal residue modification mass">0.0</note>
        <note type="input" label="protein, cleavage C-terminal mass change">+17.00305</note>
        <note type="input" label="protein, cleavage N-terminal mass change">+1.00794</note>
        <note type="input" label="protein, cleavage semi">no</note>
        <note type="input" label="protein, cleavage site">[RK]|{P}</note>
        <note type="input" label="protein, modified residue mass file"/>
        <note type="input" label="protein, quick acetyl">yes</note>
        <note type="input" label="protein, quick pyrolidone">yes</note>
        <note type="input" label="protein, stP bias">yes</note>
        <note type="input" label="protein, taxon">usedefined</note>
        <note type="input" label="protein, use minimal annotations">yes</note>
        <note type="input" label="refine">yes</note>
        <note type="input" label="refine, cleavage semi">yes</note>
        <note type="input" label="refine, maximum missed cleavage sites">3</note>
        <note type="input" label="refine, maximum valid expectation value">0.01</note>
        <note type="input" label="refine, modification mass">57.02146@C</note>
        <note type="input" label="refine, modification mass 1"/>
        <note type="input" label="refine, point mutations">no</note>
        <note type="input" label="refine, potential C-terminus modifications"/>
        <note type="input" label="refine, potential N-terminus modifications"/>
        <note type="input" label="refine, potential modification mass">15.99491@M</note>
        <note type="input" label="refine, potential modification mass 1"/>
        <note type="input" label="refine, potential modification motif"/>
        <note type="input" label="refine, potential modification motif 1"/>
        <note type="input" label="refine, spectrum synthesis">yes</note>
        <note type="input" label="refine, unanticipated cleavage">no</note>
        <note type="input" label="refine, use potential modifications for full refinement">yes</note>
        <note type="input" label="residue, modification mass">57.02146@C</note>
        <note type="input" label="residue, modification mass 1"/>
        <note type="input" label="residue, potential modification mass">15.99491@M</note>
        <note type="input" label="residue, potential modification motif"/>
        <note type="input" label="refine, maximum missed cleavage sites">3</note>
        <note type="input" label="scoring, a ions">no</note>
        <note type="input" label="scoring, b ions">yes</note>
        <note type="input" label="scoring, c ions">no</note>
        <note type="input" label="scoring, cyclic permutation">yes</note>
        <note type="input" label="scoring, include reverse">yes</note>
        <note type="input" label="scoring, maximum missed cleavage sites">1</note>
        <note type="input" label="scoring, minimum ion count">4</note>
        <note type="input" label="scoring, x ions">no</note>
        <note type="input" label="scoring, y ions">yes</note>
        <note type="input" label="scoring, z ions">no</note>
        <note type="input" label="spectrum, dynamic range">100</note>
        <note type="input" label="spectrum, fragment mass type">monoisotopic</note>
        <note type="input" label="spectrum, fragment monoisotopic mass error">0.02</note>
        <note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
        <note type="input" label="spectrum, maximum parent charge">4</note>
        <note type="input" label="spectrum, minimum fragment mz">150</note>
        <note type="input" label="spectrum, minimum parent m+h">300</note>
        <note type="input" label="spectrum, minimum peaks">15</note>
        <note type="input" label="spectrum, parent monoisotopic mass error minus">15</note>
        <note type="input" label="spectrum, parent monoisotopic mass error plus">15</note>
        <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
        <note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
        <note type="input" label="output, spectrum index">true</note>
        <note type="input" label="spectrum, timstof MS2 filters">chargeDeconvolution|0.02dalton mzExclusion|0.01dalton</note>
        <note type="input" label="spectrum, sequence batch size">1000</note>
        <note type="input" label="spectrum, threads">6</note>
        <note type="input" label="spectrum, total peaks">100</note>
        <note type="input" label="spectrum, use contrast angle">no</note>
        <note type="input" label="spectrum, use neutral loss window">no</note>
    </group>
</bioml>
