<macros>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Job Failed" />
            <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
            <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
        </stdio>
    </xml>
    <token name="@GENERAL_PARAMETERS@">
            -frag_tol "${fragment_tol}"
            -prec_tol "${precursor_ion_tol}"
            -prec_ppm "${precursor_ion_tol_units}"
            -enzyme "${enzyme}"
            #set $fixed_mods_str = $fixed_modifications or ''
            #set $variable_mods_str = $variable_modifications or ''
            #if $fixed_mods_str
                -fixed_mods "$fixed_mods_str" 
            #end if
            #if $variable_mods_str
                -variable_mods "$variable_mods_str"
            #end if
            -min_charge $min_charge
            -max_charge $max_charge
            -mc $missed_cleavages
            -fi $forward_ion
            -ri $reverse_ion
    </token>

    <xml name="general_options">
        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
            help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
            <option value="1">Parts per million (ppm)</option>
            <option value="2">Daltons</option>
        </param>
        <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
            help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
        <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
            help="Provide error value for fragment ions, based on instrument used"/>
        <param name="enzyme" type="select" label="Enzyme"
            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
            <option value="Trypsin">Trypsin</option>
            <option value="Arg-C">Arg-C</option>
            <option value="CNBr">CNBr</option>
            <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
            <option value="Formic Acid">Formic Acid</option>
            <option value="Lys-C">Lys-C</option>
            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
            <option value="Pepsin A">Pepsin A</option>
            <option value="Trypsin + CNBr">Trypsin + CNBr</option>
            <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
            <option value="Trypsin, no P rule">Trypsin, no P rule</option>
            <option value="whole protein">whole protein</option>
            <option value="Asp-N">Asp-N</option>
            <option value="Glu-C">Glu-C</option>
            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
            <option value="Top-Down">Top-Down</option>
            <option value="Semi-Tryptic">Semi-Tryptic</option>
            <option value="No enzyme">No enzyme</option>
            <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
            <option value="Asp-N (DE)">Asp-N (DE)</option>
            <option value="Glu-C (DE)">Glu-C (DE)</option>
            <option value="Lys-N (K)">Lys-N (K)</option>
            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
            <option value="Semi-Glu-C">Semi-Glu-C</option>
        </param>
        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
        <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
            help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
            <options from_file="searchgui_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="0" />
            </options>
        </param>
        <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" 
            help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
            <options from_file="searchgui_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="0" />
            </options>
        </param>
        <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
        <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
        <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
            <option value="a">a</option>
            <option value="b" selected="true">b</option>
            <option value="c">c</option>
        </param>
        <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
            <option value="x">x</option>
            <option value="y" selected="true">y</option>
            <option value="z">z</option>
        </param>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/1471-2105-12-70</citation>
            <citation type="doi">10.1002/pmic.201000595</citation>
            <citation type="doi">doi:10.1038/nbt.3109</citation>
        </citations>
    </xml>

</macros>