comparison macros.xml @ 18:ffed32e397cb draft

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17:2f8e9d0351a8

    <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}"

            -max_charge $max_charge
            -mc $missed_cleavages
            -fi $forward_ion
            -ri $reverse_ion
    </token>
    <token name="@SEARCHGUI_MAJOR_VERSION@">2</token>
    <token name="@SEARCHGUI_VERSION@">2.9</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>

18:ffed32e397cb

    <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"/>
            <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
        </stdio>
    </xml>
    <token name="@GENERAL_PARAMETERS@">
            -frag_tol "${fragment_tol}"
            -prec_tol "${precursor_ion_tol}"

            -max_charge $max_charge
            -mc $missed_cleavages
            -fi $forward_ion
            -ri $reverse_ion
    </token>
    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
    <token name="@SEARCHGUI_VERSION@">3.1.4</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>