view macros.xml @ 4:9cb7dcc07dae draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
author galaxyp
date Fri, 19 Feb 2021 21:25:06 +0000
parents 2d67fb758956
children
line wrap: on
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<?xml version="1.0" ?>
<macros>
    <token name="@VERSION@">1.6.10.43</token>
    <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
    <token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
                    - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]
                    - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]
                    - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]
                    - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True]
                    - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True]
                    - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True]
                    - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]
                    - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]
                    - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]
    ]]></token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">maxquant</requirement>
            <requirement type="package" version="3.7">python</requirement>
            <requirement type="package" version="5.1.2">pyyaml</requirement>
            <requirement type="package" version="0.92.6">r-ptxqc</requirement>
            <requirement type="package" version="1.32">tar</requirement>
        </requirements>
    </xml>
    
    <xml name="ptxqc">
        <configfile name="qr_yaml">
            PTXQC:
              ReportFilename:
                extended: yes
              UseLocalMQPar: yes
              NameLengthMax_num: 10.0
              OutputFormats:
              - plainPDF
              PlainPDF:
                AddPageNumbers: 'on'
            File:
              Parameters:
              #if $qc.do_it:
                enabled: ${qc.parameters}
              #end if
              Summary:
              #if $qc.do_it:
                enabled: ${qc.summary}
              #end if
                IDRate:
                  Thresh_bad_num: 20.0
                  Thresh_great_num: 35.0
              ProteinGroups:
              #if $qc.do_it:
                enabled: ${qc.proteingroups}
              #end if
                RatioPlot:
                  LabelIncThresh_num: 4.0
                IntensityThreshLog2_num: 25.0
              Evidence:
              #if $qc.do_it:
                enabled: ${qc.evidence}
              #end if
                ProteinCountThresh_num: 3500.0
                IntensityThreshLog2_num: 23.0
                PeptideCountThresh_num: 15000.0
                SpecialContaminants:
                  cont_MYCO:
                  - MYCOPLASMA
                  - '1'
                MQpar_MatchingTimeWindow_num: 0.0
                MatchBetweenRuns_wA: auto
                MQpar_firstSearchTol_num: 20.0
                firstSearch_outOfCalWarnSD_num: 2.0
                MQpar_mainSearchTol_num: 4.5
              MsMs:
              #if $qc.do_it:
                enabled: ${qc.msms}
              #end if
              MsMsScans:
              #if $qc.do_it:
                enabled: ${qc.msmsscans}
              #end if
                IonInjectionThresh_num: 10.0
            order:
              qcMetric_PAR: 1.0
              qcMetric_PG_PCA: 3.0
              qcMetric_EVD_Top5Cont: 10.0
              qcMetric_PG_Ratio: 19.0
              qcMetric_EVD_UserContaminant: 20.0
              qcMetric_EVD_PeptideInt: 30.0
              qcMetric_EVD_ReporterInt: 31.0
              qcMetric_PG_RawInt: 32.0
              qcMetric_PG_LFQInt: 33.0
              qcMetric_PG_ReporterInt: 34.0
              qcMetric_MSMS_MissedCleavages: 40.0
              qcMetric_EVD_Charge: 100.0
              qcMetric_PG_Cont: 110.0
              qcMetric_MSMSScans_TopNoverRT: 120.0
              qcMetric_EVD_IDoverRT: 150.0
              qcMetric_EVD_RTPeakWidth: 170.0
              qcMetric_EVD_MBRAlign: 210.0
              qcMetric_EVD_MBRIdTransfer: 220.0
              qcMetric_EVD_MBRaux: 221.0
              qcMetric_MSMSScans_IonInjTime: 240.0
              qcMetric_MSMSScans_MSMSIntensity: 245.0
              qcMetric_EVD_MS2OverSampling: 250.0
              qcMetric_EVD_PreCal: 260.0
              qcMetric_EVD_PostCal: 270.0
              qcMetric_MSMS_MSMSDecal: 280.0
              qcMetric_SM_MSMSIdRate: 300.0
              qcMetric_MSMSScans_TopNID: 380.0
              qcMetric_MSMSScans_DepPep: 383.0
              qcMetric_EVD_MissingValues: 390.0
              qcMetric_EVD_PeptideCount: 400.0
              qcMetric_EVD_ProteinCount: 450.0
              qcMetric_AverageQualOverall: 9999.0
        </configfile>
        <configfile name="qr">
            library(PTXQC)
            library(yaml)
            library(methods)
            args = commandArgs(trailingOnly=TRUE)
            yaml_config = yaml.load_file(input = args[1])
            r = createReport('./combined/txt', yaml_config)
            cat(paste0("\nReport generated as '", r\$report_file, "'\n\n"))
        </configfile>
    </xml>

    <xml name="mod_option" token_value="default">
        <option value="@VALUE@">@VALUE@</option>
    </xml>
    <xml name="default_mod_option" token_value="default">
        <option selected="true" value="@VALUE@">@VALUE@</option>
    </xml>

    <xml name="ptxqc-opts">
        <conditional name="qc">
            <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)"
                   type="boolean" checked="false"/>
            <when value="true">
                <param name="parameters" type="boolean" checked="true"
	               label="use parameters.txt?" truevalue="yes" falsevalue="no" />
                <param name="summary" type="boolean" checked="true"
	               label="use summary.txt?" truevalue="yes" falsevalue="no" />
                <param name="proteingroups" type="boolean" checked="true"
	               label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" />
                <param name="evidence" type="boolean" checked="true"
	               label="use evidence.txt?" truevalue="yes" falsevalue="no" />
                <param name="msms" type="boolean" checked="true"
	               label="use msms.txt?" truevalue="yes" falsevalue="no" />
                <param name="msmsscans" type="boolean" checked="true"
	               label="use msmsScans.txt?" truevalue="yes" falsevalue="no" />
            </when>
            <when value="false"/>
        </conditional>
    </xml>
    
    <xml name="outputs">
        <outputs>
            <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>
            <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/>
            <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/>
            <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/>
            <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/>
            <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/>
            <expand macro="output_from_wdir" name="mzTab" label="mzTab" ext="mzTab"/>
            <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/>
            <expand macro="output_from_wdir" name="libraryMatch" label="library match"/>
            <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/>
            <expand macro="output_from_wdir" name="modificationSpecificPeptides" label="modification specific peptides"/>
            <expand macro="output_from_wdir" name="ms3Scans" label="ms3 scans"/>
            <expand macro="output_from_wdir" name="msmsScans" label="msms Scans"/>
            <expand macro="output_from_wdir" name="mzRange" label="mz range"/>
            <expand macro="output_from_wdir" name="peptideSection" label="peptide section"/>
            <expand macro="output_from_wdir" name="summary" label="MaxQuant summary"/>
            <expand macro="output" name="output_all" format="tar" label="'combined/txt/' directory"/>
            <expand macro="output" name="log" format="txt" label="log"/>
            <expand macro="output" name="config" format="txt" label="yaml config file"/>
            <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">
                <filter>qc['do_it'] == True</filter>
            </data>
        </outputs>
    </xml>
    
    <xml name="modification">
        <expand macro="mod_option" value="Acetyl (K)"/>
        <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
        <expand macro="mod_option" value="Carbamidomethyl (C)"/>
        <expand macro="mod_option" value="Oxidation (M)"/>
        <expand macro="mod_option" value="Phospho (STY)"/>
        <expand macro="mod_option" value="GlyGly (K)"/>
        <expand macro="mod_option" value="Methyl (KR)"/>
        <expand macro="mod_option" value="Dimethyl (KR)"/>
        <expand macro="mod_option" value="Trimethyl (K)"/>
        <expand macro="mod_option" value="Pro5"/>
        <expand macro="mod_option" value="Pro6"/>
        <expand macro="mod_option" value="Glu-&gt;pyro-Glu"/>
        <expand macro="mod_option" value="Gln-&gt;pyro-Glu"/>
        <expand macro="mod_option" value="QQTGG (K)"/>
        <expand macro="mod_option" value="Deamidation (N)"/>
        <expand macro="mod_option" value="Deamidation 18O (N)"/>
        <expand macro="mod_option" value="Deamidation (NQ)"/>
        <expand macro="mod_option" value="Hydroxyproline"/>
        <expand macro="mod_option" value="Carbamyl (N-term)"/>
        <expand macro="mod_option" value="Delta:H(2)C(2) (N-term)"/>
        <expand macro="mod_option" value="Dioxidation (MW)"/>
        <expand macro="mod_option" value="Trioxidation (C)"/>
        <expand macro="mod_option" value="Dethiomethyl (M)"/>
        <expand macro="mod_option" value="Cation:Na (DE)"/>
        <expand macro="mod_option" value="Methyl (E)"/>
        <expand macro="mod_option" value="Dehydrated (ST)"/>
        <expand macro="mod_option" value="Oxidation (P)"/>
        <expand macro="mod_option" value="Dimethyl (K)"/>
        <expand macro="mod_option" value="Amidated (Protein C-term)"/>
        <expand macro="mod_option" value="Sulfo (STY)"/>
        <expand macro="mod_option" value="Acetyl (N-term)"/>
        <expand macro="mod_option" value="Amidated (C-term)"/>
        <expand macro="mod_option" value="Sulfation (Y)"/>
        <expand macro="mod_option" value="Phospho (ST)"/>
        <expand macro="mod_option" value="Cys-Cys"/>
        <expand macro="mod_option" value="Ala-&gt;Arg"/>
        <expand macro="mod_option" value="Ala-&gt;Asn"/>
        <expand macro="mod_option" value="Ala-&gt;Asp"/>
        <expand macro="mod_option" value="Ala-&gt;Cys"/>
        <expand macro="mod_option" value="Ala-&gt;Gln"/>
        <expand macro="mod_option" value="Ala-&gt;Glu"/>
        <expand macro="mod_option" value="Ala-&gt;Gly"/>
        <expand macro="mod_option" value="Ala-&gt;His"/>
        <expand macro="mod_option" value="Ala-&gt;Xle"/>
        <expand macro="mod_option" value="Ala-&gt;Lys"/>
        <expand macro="mod_option" value="Ala-&gt;Met"/>
        <expand macro="mod_option" value="Ala-&gt;Phe"/>
        <expand macro="mod_option" value="Ala-&gt;Pro"/>
        <expand macro="mod_option" value="Ala-&gt;Ser"/>
        <expand macro="mod_option" value="Ala-&gt;Thr"/>
        <expand macro="mod_option" value="Ala-&gt;Trp"/>
        <expand macro="mod_option" value="Ala-&gt;Tyr"/>
        <expand macro="mod_option" value="Ala-&gt;Val"/>
        <expand macro="mod_option" value="Arg-&gt;Ala"/>
        <expand macro="mod_option" value="Arg-&gt;Asn"/>
        <expand macro="mod_option" value="Arg-&gt;Asp"/>
        <expand macro="mod_option" value="Arg-&gt;Cys"/>
        <expand macro="mod_option" value="Arg-&gt;Gln"/>
        <expand macro="mod_option" value="Arg-&gt;Glu"/>
        <expand macro="mod_option" value="Arg-&gt;Gly"/>
        <expand macro="mod_option" value="Arg-&gt;His"/>
        <expand macro="mod_option" value="Arg-&gt;Lys"/>
        <expand macro="mod_option" value="Arg-&gt;Met"/>
        <expand macro="mod_option" value="Arg-&gt;Phe"/>
        <expand macro="mod_option" value="Arg-&gt;Pro"/>
        <expand macro="mod_option" value="Arg-&gt;Ser"/>
        <expand macro="mod_option" value="Arg-&gt;Thr"/>
        <expand macro="mod_option" value="Arg-&gt;Trp"/>
        <expand macro="mod_option" value="Arg-&gt;Tyr"/>
        <expand macro="mod_option" value="Arg-&gt;Val"/>
        <expand macro="mod_option" value="Arg-&gt;Xle"/>
        <expand macro="mod_option" value="Asn-&gt;Ala"/>
        <expand macro="mod_option" value="Asn-&gt;Arg"/>
        <expand macro="mod_option" value="Asn-&gt;Asp"/>
        <expand macro="mod_option" value="Asn-&gt;Cys"/>
        <expand macro="mod_option" value="Asn-&gt;Gln"/>
        <expand macro="mod_option" value="Asn-&gt;Glu"/>
        <expand macro="mod_option" value="Asn-&gt;Gly"/>
        <expand macro="mod_option" value="Asn-&gt;His"/>
        <expand macro="mod_option" value="Asn-&gt;Lys"/>
        <expand macro="mod_option" value="Asn-&gt;Met"/>
        <expand macro="mod_option" value="Asn-&gt;Phe"/>
        <expand macro="mod_option" value="Asn-&gt;Pro"/>
        <expand macro="mod_option" value="Asn-&gt;Ser"/>
        <expand macro="mod_option" value="Asn-&gt;Thr"/>
        <expand macro="mod_option" value="Asn-&gt;Trp"/>
        <expand macro="mod_option" value="Asn-&gt;Tyr"/>
        <expand macro="mod_option" value="Asn-&gt;Val"/>
        <expand macro="mod_option" value="Asn-&gt;Xle"/>
        <expand macro="mod_option" value="Asp-&gt;Ala"/>
        <expand macro="mod_option" value="Asp-&gt;Arg"/>
        <expand macro="mod_option" value="Asp-&gt;Asn"/>
        <expand macro="mod_option" value="Asp-&gt;Cys"/>
        <expand macro="mod_option" value="Asp-&gt;Gln"/>
        <expand macro="mod_option" value="Asp-&gt;Glu"/>
        <expand macro="mod_option" value="Asp-&gt;Gly"/>
        <expand macro="mod_option" value="Asp-&gt;His"/>
        <expand macro="mod_option" value="Asp-&gt;Lys"/>
        <expand macro="mod_option" value="Asp-&gt;Met"/>
        <expand macro="mod_option" value="Asp-&gt;Phe"/>
        <expand macro="mod_option" value="Asp-&gt;Pro"/>
        <expand macro="mod_option" value="Asp-&gt;Ser"/>
        <expand macro="mod_option" value="Asp-&gt;Thr"/>
        <expand macro="mod_option" value="Asp-&gt;Trp"/>
        <expand macro="mod_option" value="Asp-&gt;Tyr"/>
        <expand macro="mod_option" value="Asp-&gt;Val"/>
        <expand macro="mod_option" value="Asp-&gt;Xle"/>
        <expand macro="mod_option" value="Cys-&gt;Ala"/>
        <expand macro="mod_option" value="Cys-&gt;Arg"/>
        <expand macro="mod_option" value="Cys-&gt;Asn"/>
        <expand macro="mod_option" value="Cys-&gt;Asp"/>
        <expand macro="mod_option" value="Cys-&gt;Gln"/>
        <expand macro="mod_option" value="Cys-&gt;Glu"/>
        <expand macro="mod_option" value="Cys-&gt;Gly"/>
        <expand macro="mod_option" value="Cys-&gt;His"/>
        <expand macro="mod_option" value="Cys-&gt;Lys"/>
        <expand macro="mod_option" value="Cys-&gt;Met"/>
        <expand macro="mod_option" value="Cys-&gt;Phe"/>
        <expand macro="mod_option" value="Cys-&gt;Pro"/>
        <expand macro="mod_option" value="Cys-&gt;Ser"/>
        <expand macro="mod_option" value="Cys-&gt;Thr"/>
        <expand macro="mod_option" value="Cys-&gt;Trp"/>
        <expand macro="mod_option" value="Cys-&gt;Tyr"/>
        <expand macro="mod_option" value="Cys-&gt;Val"/>
        <expand macro="mod_option" value="Cys-&gt;Xle"/>
        <expand macro="mod_option" value="Gln-&gt;Ala"/>
        <expand macro="mod_option" value="Gln-&gt;Arg"/>
        <expand macro="mod_option" value="Gln-&gt;Asn"/>
        <expand macro="mod_option" value="Gln-&gt;Asp"/>
        <expand macro="mod_option" value="Gln-&gt;Cys"/>
        <expand macro="mod_option" value="Gln-&gt;Glu"/>
        <expand macro="mod_option" value="Gln-&gt;Gly"/>
        <expand macro="mod_option" value="Gln-&gt;His"/>
        <expand macro="mod_option" value="Gln-&gt;Lys"/>
        <expand macro="mod_option" value="Gln-&gt;Met"/>
        <expand macro="mod_option" value="Gln-&gt;Phe"/>
        <expand macro="mod_option" value="Gln-&gt;Pro"/>
        <expand macro="mod_option" value="Gln-&gt;Ser"/>
        <expand macro="mod_option" value="Gln-&gt;Thr"/>
        <expand macro="mod_option" value="Gln-&gt;Trp"/>
        <expand macro="mod_option" value="Gln-&gt;Tyr"/>
        <expand macro="mod_option" value="Gln-&gt;Val"/>
        <expand macro="mod_option" value="Gln-&gt;Xle"/>
        <expand macro="mod_option" value="Glu-&gt;Ala"/>
        <expand macro="mod_option" value="Glu-&gt;Arg"/>
        <expand macro="mod_option" value="Glu-&gt;Asn"/>
        <expand macro="mod_option" value="Glu-&gt;Asp"/>
        <expand macro="mod_option" value="Glu-&gt;Cys"/>
        <expand macro="mod_option" value="Glu-&gt;Gln"/>
        <expand macro="mod_option" value="Glu-&gt;Gly"/>
        <expand macro="mod_option" value="Glu-&gt;His"/>
        <expand macro="mod_option" value="Glu-&gt;Lys"/>
        <expand macro="mod_option" value="Glu-&gt;Met"/>
        <expand macro="mod_option" value="Glu-&gt;Phe"/>
        <expand macro="mod_option" value="Glu-&gt;Pro"/>
        <expand macro="mod_option" value="Glu-&gt;Ser"/>
        <expand macro="mod_option" value="Glu-&gt;Thr"/>
        <expand macro="mod_option" value="Glu-&gt;Trp"/>
        <expand macro="mod_option" value="Glu-&gt;Tyr"/>
        <expand macro="mod_option" value="Glu-&gt;Val"/>
        <expand macro="mod_option" value="Glu-&gt;Xle"/>
        <expand macro="mod_option" value="Gly-&gt;Ala"/>
        <expand macro="mod_option" value="Gly-&gt;Arg"/>
        <expand macro="mod_option" value="Gly-&gt;Asn"/>
        <expand macro="mod_option" value="Gly-&gt;Asp"/>
        <expand macro="mod_option" value="Gly-&gt;Cys"/>
        <expand macro="mod_option" value="Gly-&gt;Gln"/>
        <expand macro="mod_option" value="Gly-&gt;Glu"/>
        <expand macro="mod_option" value="Gly-&gt;His"/>
        <expand macro="mod_option" value="Gly-&gt;Lys"/>
        <expand macro="mod_option" value="Gly-&gt;Met"/>
        <expand macro="mod_option" value="Gly-&gt;Phe"/>
        <expand macro="mod_option" value="Gly-&gt;Pro"/>
        <expand macro="mod_option" value="Gly-&gt;Ser"/>
        <expand macro="mod_option" value="Gly-&gt;Thr"/>
        <expand macro="mod_option" value="Gly-&gt;Trp"/>
        <expand macro="mod_option" value="Gly-&gt;Tyr"/>
        <expand macro="mod_option" value="Gly-&gt;Val"/>
        <expand macro="mod_option" value="Gly-&gt;Xle"/>
        <expand macro="mod_option" value="His-&gt;Ala"/>
        <expand macro="mod_option" value="His-&gt;Arg"/>
        <expand macro="mod_option" value="His-&gt;Asn"/>
        <expand macro="mod_option" value="His-&gt;Asp"/>
        <expand macro="mod_option" value="His-&gt;Cys"/>
        <expand macro="mod_option" value="His-&gt;Gln"/>
        <expand macro="mod_option" value="His-&gt;Glu"/>
        <expand macro="mod_option" value="His-&gt;Gly"/>
        <expand macro="mod_option" value="His-&gt;Lys"/>
        <expand macro="mod_option" value="His-&gt;Met"/>
        <expand macro="mod_option" value="His-&gt;Phe"/>
        <expand macro="mod_option" value="His-&gt;Pro"/>
        <expand macro="mod_option" value="His-&gt;Ser"/>
        <expand macro="mod_option" value="His-&gt;Thr"/>
        <expand macro="mod_option" value="His-&gt;Trp"/>
        <expand macro="mod_option" value="His-&gt;Tyr"/>
        <expand macro="mod_option" value="His-&gt;Val"/>
        <expand macro="mod_option" value="His-&gt;Xle"/>
        <expand macro="mod_option" value="Lys-&gt;Ala"/>
        <expand macro="mod_option" value="Lys-&gt;Arg"/>
        <expand macro="mod_option" value="Lys-&gt;Asn"/>
        <expand macro="mod_option" value="Lys-&gt;Asp"/>
        <expand macro="mod_option" value="Lys-&gt;Cys"/>
        <expand macro="mod_option" value="Lys-&gt;Gln"/>
        <expand macro="mod_option" value="Lys-&gt;Glu"/>
        <expand macro="mod_option" value="Lys-&gt;Gly"/>
        <expand macro="mod_option" value="Lys-&gt;His"/>
        <expand macro="mod_option" value="Lys-&gt;Met"/>
        <expand macro="mod_option" value="Lys-&gt;Phe"/>
        <expand macro="mod_option" value="Lys-&gt;Pro"/>
        <expand macro="mod_option" value="Lys-&gt;Ser"/>
        <expand macro="mod_option" value="Lys-&gt;Thr"/>
        <expand macro="mod_option" value="Lys-&gt;Trp"/>
        <expand macro="mod_option" value="Lys-&gt;Tyr"/>
        <expand macro="mod_option" value="Lys-&gt;Val"/>
        <expand macro="mod_option" value="Lys-&gt;Xle"/>
        <expand macro="mod_option" value="Met-&gt;Ala"/>
        <expand macro="mod_option" value="Met-&gt;Arg"/>
        <expand macro="mod_option" value="Met-&gt;Asn"/>
        <expand macro="mod_option" value="Met-&gt;Asp"/>
        <expand macro="mod_option" value="Met-&gt;Cys"/>
        <expand macro="mod_option" value="Met-&gt;Gln"/>
        <expand macro="mod_option" value="Met-&gt;Glu"/>
        <expand macro="mod_option" value="Met-&gt;Gly"/>
        <expand macro="mod_option" value="Met-&gt;His"/>
        <expand macro="mod_option" value="Met-&gt;Lys"/>
        <expand macro="mod_option" value="Met-&gt;Phe"/>
        <expand macro="mod_option" value="Met-&gt;Pro"/>
        <expand macro="mod_option" value="Met-&gt;Ser"/>
        <expand macro="mod_option" value="Met-&gt;Thr"/>
        <expand macro="mod_option" value="Met-&gt;Trp"/>
        <expand macro="mod_option" value="Met-&gt;Tyr"/>
        <expand macro="mod_option" value="Met-&gt;Val"/>
        <expand macro="mod_option" value="Met-&gt;Xle"/>
        <expand macro="mod_option" value="Phe-&gt;Ala"/>
        <expand macro="mod_option" value="Phe-&gt;Arg"/>
        <expand macro="mod_option" value="Phe-&gt;Asn"/>
        <expand macro="mod_option" value="Phe-&gt;Asp"/>
        <expand macro="mod_option" value="Phe-&gt;Cys"/>
        <expand macro="mod_option" value="Phe-&gt;Gln"/>
        <expand macro="mod_option" value="Phe-&gt;Glu"/>
        <expand macro="mod_option" value="Phe-&gt;Gly"/>
        <expand macro="mod_option" value="Phe-&gt;His"/>
        <expand macro="mod_option" value="Phe-&gt;Lys"/>
        <expand macro="mod_option" value="Phe-&gt;Met"/>
        <expand macro="mod_option" value="Phe-&gt;Pro"/>
        <expand macro="mod_option" value="Phe-&gt;Ser"/>
        <expand macro="mod_option" value="Phe-&gt;Thr"/>
        <expand macro="mod_option" value="Phe-&gt;Trp"/>
        <expand macro="mod_option" value="Phe-&gt;Tyr"/>
        <expand macro="mod_option" value="Phe-&gt;Val"/>
        <expand macro="mod_option" value="Phe-&gt;Xle"/>
        <expand macro="mod_option" value="Pro-&gt;Ala"/>
        <expand macro="mod_option" value="Pro-&gt;Arg"/>
        <expand macro="mod_option" value="Pro-&gt;Asn"/>
        <expand macro="mod_option" value="Pro-&gt;Asp"/>
        <expand macro="mod_option" value="Pro-&gt;Cys"/>
        <expand macro="mod_option" value="Pro-&gt;Gln"/>
        <expand macro="mod_option" value="Pro-&gt;Glu"/>
        <expand macro="mod_option" value="Pro-&gt;Gly"/>
        <expand macro="mod_option" value="Pro-&gt;His"/>
        <expand macro="mod_option" value="Pro-&gt;Lys"/>
        <expand macro="mod_option" value="Pro-&gt;Met"/>
        <expand macro="mod_option" value="Pro-&gt;Phe"/>
        <expand macro="mod_option" value="Pro-&gt;Ser"/>
        <expand macro="mod_option" value="Pro-&gt;Thr"/>
        <expand macro="mod_option" value="Pro-&gt;Trp"/>
        <expand macro="mod_option" value="Pro-&gt;Tyr"/>
        <expand macro="mod_option" value="Pro-&gt;Val"/>
        <expand macro="mod_option" value="Pro-&gt;Xle"/>
        <expand macro="mod_option" value="Ser-&gt;Ala"/>
        <expand macro="mod_option" value="Ser-&gt;Arg"/>
        <expand macro="mod_option" value="Ser-&gt;Asn"/>
        <expand macro="mod_option" value="Ser-&gt;Asp"/>
        <expand macro="mod_option" value="Ser-&gt;Cys"/>
        <expand macro="mod_option" value="Ser-&gt;Gln"/>
        <expand macro="mod_option" value="Ser-&gt;Glu"/>
        <expand macro="mod_option" value="Ser-&gt;Gly"/>
        <expand macro="mod_option" value="Ser-&gt;His"/>
        <expand macro="mod_option" value="Ser-&gt;Lys"/>
        <expand macro="mod_option" value="Ser-&gt;Met"/>
        <expand macro="mod_option" value="Ser-&gt;Phe"/>
        <expand macro="mod_option" value="Ser-&gt;Pro"/>
        <expand macro="mod_option" value="Ser-&gt;Thr"/>
        <expand macro="mod_option" value="Ser-&gt;Trp"/>
        <expand macro="mod_option" value="Ser-&gt;Tyr"/>
        <expand macro="mod_option" value="Ser-&gt;Val"/>
        <expand macro="mod_option" value="Ser-&gt;Xle"/>
        <expand macro="mod_option" value="Thr-&gt;Ala"/>
        <expand macro="mod_option" value="Thr-&gt;Arg"/>
        <expand macro="mod_option" value="Thr-&gt;Asn"/>
        <expand macro="mod_option" value="Thr-&gt;Asp"/>
        <expand macro="mod_option" value="Thr-&gt;Cys"/>
        <expand macro="mod_option" value="Thr-&gt;Gln"/>
        <expand macro="mod_option" value="Thr-&gt;Glu"/>
        <expand macro="mod_option" value="Thr-&gt;Gly"/>
        <expand macro="mod_option" value="Thr-&gt;His"/>
        <expand macro="mod_option" value="Thr-&gt;Lys"/>
        <expand macro="mod_option" value="Thr-&gt;Met"/>
        <expand macro="mod_option" value="Thr-&gt;Phe"/>
        <expand macro="mod_option" value="Thr-&gt;Pro"/>
        <expand macro="mod_option" value="Thr-&gt;Ser"/>
        <expand macro="mod_option" value="Thr-&gt;Trp"/>
        <expand macro="mod_option" value="Thr-&gt;Tyr"/>
        <expand macro="mod_option" value="Thr-&gt;Val"/>
        <expand macro="mod_option" value="Thr-&gt;Xle"/>
        <expand macro="mod_option" value="Trp-&gt;Ala"/>
        <expand macro="mod_option" value="Trp-&gt;Arg"/>
        <expand macro="mod_option" value="Trp-&gt;Asn"/>
        <expand macro="mod_option" value="Trp-&gt;Asp"/>
        <expand macro="mod_option" value="Trp-&gt;Cys"/>
        <expand macro="mod_option" value="Trp-&gt;Gln"/>
        <expand macro="mod_option" value="Trp-&gt;Glu"/>
        <expand macro="mod_option" value="Trp-&gt;Gly"/>
        <expand macro="mod_option" value="Trp-&gt;His"/>
        <expand macro="mod_option" value="Trp-&gt;Lys"/>
        <expand macro="mod_option" value="Trp-&gt;Met"/>
        <expand macro="mod_option" value="Trp-&gt;Phe"/>
        <expand macro="mod_option" value="Trp-&gt;Pro"/>
        <expand macro="mod_option" value="Trp-&gt;Ser"/>
        <expand macro="mod_option" value="Trp-&gt;Thr"/>
        <expand macro="mod_option" value="Trp-&gt;Tyr"/>
        <expand macro="mod_option" value="Trp-&gt;Val"/>
        <expand macro="mod_option" value="Trp-&gt;Xle"/>
        <expand macro="mod_option" value="Tyr-&gt;Ala"/>
        <expand macro="mod_option" value="Tyr-&gt;Arg"/>
        <expand macro="mod_option" value="Tyr-&gt;Asn"/>
        <expand macro="mod_option" value="Tyr-&gt;Asp"/>
        <expand macro="mod_option" value="Tyr-&gt;Cys"/>
        <expand macro="mod_option" value="Tyr-&gt;Gln"/>
        <expand macro="mod_option" value="Tyr-&gt;Glu"/>
        <expand macro="mod_option" value="Tyr-&gt;Gly"/>
        <expand macro="mod_option" value="Tyr-&gt;His"/>
        <expand macro="mod_option" value="Tyr-&gt;Lys"/>
        <expand macro="mod_option" value="Tyr-&gt;Met"/>
        <expand macro="mod_option" value="Tyr-&gt;Phe"/>
        <expand macro="mod_option" value="Tyr-&gt;Pro"/>
        <expand macro="mod_option" value="Tyr-&gt;Ser"/>
        <expand macro="mod_option" value="Tyr-&gt;Thr"/>
        <expand macro="mod_option" value="Tyr-&gt;Trp"/>
        <expand macro="mod_option" value="Tyr-&gt;Val"/>
        <expand macro="mod_option" value="Tyr-&gt;Xle"/>
        <expand macro="mod_option" value="Val-&gt;Ala"/>
        <expand macro="mod_option" value="Val-&gt;Arg"/>
        <expand macro="mod_option" value="Val-&gt;Asn"/>
        <expand macro="mod_option" value="Val-&gt;Asp"/>
        <expand macro="mod_option" value="Val-&gt;Cys"/>
        <expand macro="mod_option" value="Val-&gt;Gln"/>
        <expand macro="mod_option" value="Val-&gt;Glu"/>
        <expand macro="mod_option" value="Val-&gt;Gly"/>
        <expand macro="mod_option" value="Val-&gt;His"/>
        <expand macro="mod_option" value="Val-&gt;Lys"/>
        <expand macro="mod_option" value="Val-&gt;Met"/>
        <expand macro="mod_option" value="Val-&gt;Phe"/>
        <expand macro="mod_option" value="Val-&gt;Pro"/>
        <expand macro="mod_option" value="Val-&gt;Ser"/>
        <expand macro="mod_option" value="Val-&gt;Thr"/>
        <expand macro="mod_option" value="Val-&gt;Trp"/>
        <expand macro="mod_option" value="Val-&gt;Tyr"/>
        <expand macro="mod_option" value="Val-&gt;Xle"/>
        <expand macro="mod_option" value="Xle-&gt;Ala"/>
        <expand macro="mod_option" value="Xle-&gt;Arg"/>
        <expand macro="mod_option" value="Xle-&gt;Asn"/>
        <expand macro="mod_option" value="Xle-&gt;Asp"/>
        <expand macro="mod_option" value="Xle-&gt;Cys"/>
        <expand macro="mod_option" value="Xle-&gt;Gln"/>
        <expand macro="mod_option" value="Xle-&gt;Glu"/>
        <expand macro="mod_option" value="Xle-&gt;Gly"/>
        <expand macro="mod_option" value="Xle-&gt;His"/>
        <expand macro="mod_option" value="Xle-&gt;Lys"/>
        <expand macro="mod_option" value="Xle-&gt;Met"/>
        <expand macro="mod_option" value="Xle-&gt;Phe"/>
        <expand macro="mod_option" value="Xle-&gt;Pro"/>
        <expand macro="mod_option" value="Xle-&gt;Ser"/>
        <expand macro="mod_option" value="Xle-&gt;Thr"/>
        <expand macro="mod_option" value="Xle-&gt;Trp"/>
        <expand macro="mod_option" value="Xle-&gt;Tyr"/>
        <expand macro="mod_option" value="Xle-&gt;Val"/>
        <expand macro="mod_option" value="CamCys-&gt;Ala"/>
        <expand macro="mod_option" value="CamCys-&gt;Arg"/>
        <expand macro="mod_option" value="CamCys-&gt;Asn"/>
        <expand macro="mod_option" value="CamCys-&gt;Asp"/>
        <expand macro="mod_option" value="CamCys-&gt;Gln"/>
        <expand macro="mod_option" value="CamCys-&gt;Glu"/>
        <expand macro="mod_option" value="CamCys-&gt;Gly"/>
        <expand macro="mod_option" value="CamCys-&gt;His"/>
        <expand macro="mod_option" value="CamCys-&gt;Lys"/>
        <expand macro="mod_option" value="CamCys-&gt;Met"/>
        <expand macro="mod_option" value="CamCys-&gt;Phe"/>
        <expand macro="mod_option" value="CamCys-&gt;Pro"/>
        <expand macro="mod_option" value="CamCys-&gt;Ser"/>
        <expand macro="mod_option" value="CamCys-&gt;Thr"/>
        <expand macro="mod_option" value="CamCys-&gt;Trp"/>
        <expand macro="mod_option" value="CamCys-&gt;Tyr"/>
        <expand macro="mod_option" value="CamCys-&gt;Val"/>
        <expand macro="mod_option" value="CamCys-&gt;Xle"/>
        <expand macro="mod_option" value="Ala-&gt;CamCys"/>
        <expand macro="mod_option" value="Arg-&gt;CamCys"/>
        <expand macro="mod_option" value="Asn-&gt;CamCys"/>
        <expand macro="mod_option" value="Asp-&gt;CamCys"/>
        <expand macro="mod_option" value="Gln-&gt;CamCys"/>
        <expand macro="mod_option" value="Glu-&gt;CamCys"/>
        <expand macro="mod_option" value="Gly-&gt;CamCys"/>
        <expand macro="mod_option" value="His-&gt;CamCys"/>
        <expand macro="mod_option" value="Lys-&gt;CamCys"/>
        <expand macro="mod_option" value="Met-&gt;CamCys"/>
        <expand macro="mod_option" value="Phe-&gt;CamCys"/>
        <expand macro="mod_option" value="Pro-&gt;CamCys"/>
        <expand macro="mod_option" value="Ser-&gt;CamCys"/>
        <expand macro="mod_option" value="Thr-&gt;CamCys"/>
        <expand macro="mod_option" value="Trp-&gt;CamCys"/>
        <expand macro="mod_option" value="Tyr-&gt;CamCys"/>
        <expand macro="mod_option" value="Val-&gt;CamCys"/>
        <expand macro="mod_option" value="Xle-&gt;CamCys"/>
        <expand macro="mod_option" value="Cysteinyl"/>
        <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/>
    </xml>

    <xml name="label">
        <expand macro="mod_option" value="Arg6"/>
        <expand macro="mod_option" value="Arg10"/>
        <expand macro="mod_option" value="Lys4"/>
        <expand macro="mod_option" value="Lys6"/>
        <expand macro="mod_option" value="Lys8"/>
        <expand macro="mod_option" value="DimethLys0"/>
        <expand macro="mod_option" value="DimethNter0"/>
        <expand macro="mod_option" value="DimethLys4"/>
        <expand macro="mod_option" value="DimethNter4"/>
        <expand macro="mod_option" value="DimethLys8"/>
        <expand macro="mod_option" value="DimethNter8"/>
        <expand macro="mod_option" value="18O"/>
        <expand macro="mod_option" value="ICAT-0"/>
        <expand macro="mod_option" value="ICAT-9"/>
        <expand macro="mod_option" value="ICPL-Lys0"/>
        <expand macro="mod_option" value="ICPL-Nter0"/>
        <expand macro="mod_option" value="ICPL-Lys4"/>
        <expand macro="mod_option" value="ICPL-Nter4"/>
        <expand macro="mod_option" value="ICPL-Lys6"/>
        <expand macro="mod_option" value="ICPL-Nter6"/>
        <expand macro="mod_option" value="ICPL-Lys10"/>
        <expand macro="mod_option" value="ICPL-Nter10"/>
        <expand macro="mod_option" value="mTRAQ-Lys0"/>
        <expand macro="mod_option" value="mTRAQ-Nter0"/>
        <expand macro="mod_option" value="mTRAQ-Lys4"/>
        <expand macro="mod_option" value="mTRAQ-Nter4"/>
        <expand macro="mod_option" value="mTRAQ-Lys8"/>
        <expand macro="mod_option" value="mTRAQ-Nter8"/>
        <expand macro="mod_option" value="DimethLys2"/>
        <expand macro="mod_option" value="DimethNter2"/>
        <expand macro="mod_option" value="DimethLys6"/>
        <expand macro="mod_option" value="DimethNter6"/>
        <expand macro="mod_option" value="Leu7"/>
        <expand macro="mod_option" value="Ile7"/>
    </xml>

    <xml name="proteases">
        <expand macro="mod_option" value="Trypsin"/>
        <expand macro="mod_option" value="Trypsin/P"/>
        <expand macro="mod_option" value="LysC"/>
        <expand macro="mod_option" value="LysC/P"/>
        <expand macro="mod_option" value="D.P"/>
        <expand macro="mod_option" value="ArgC"/>
        <expand macro="mod_option" value="AspC"/>
        <expand macro="mod_option" value="GluC"/>
        <expand macro="mod_option" value="GluN"/>
        <expand macro="mod_option" value="AspN"/>
        <expand macro="mod_option" value="LysN"/>
        <expand macro="mod_option" value="Chymotrypsin+"/>
        <expand macro="mod_option" value="Chymotrypsin"/>
    </xml>

    <xml name="iso_labels">
        <expand macro="mod_option" value="iTRAQ4plex-Nter114"/>
        <expand macro="mod_option" value="iTRAQ4plex-Nter115"/>
        <expand macro="mod_option" value="iTRAQ4plex-Nter116"/>
        <expand macro="mod_option" value="iTRAQ4plex-Nter117"/>
        <expand macro="mod_option" value="iTRAQ4plex-Lys114"/>
        <expand macro="mod_option" value="iTRAQ4plex-Lys115"/>
        <expand macro="mod_option" value="iTRAQ4plex-Lys116"/>
        <expand macro="mod_option" value="iTRAQ4plex-Lys117"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter113"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter114"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter115"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter116"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter117"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter118"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter119"/>
        <expand macro="mod_option" value="iTRAQ8plex-Nter121"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys113"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys114"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys115"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys116"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys117"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys118"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys119"/>
        <expand macro="mod_option" value="iTRAQ8plex-Lys121"/>
        <expand macro="mod_option" value="TMT2plex-Nter126"/>
        <expand macro="mod_option" value="TMT2plex-Nter127"/>
        <expand macro="mod_option" value="TMT2plex-Lys126"/>
        <expand macro="mod_option" value="TMT2plex-Lys127"/>
        <expand macro="mod_option" value="TMT6plex-Nter126"/>
        <expand macro="mod_option" value="TMT6plex-Nter127"/>
        <expand macro="mod_option" value="TMT6plex-Nter128"/>
        <expand macro="mod_option" value="TMT6plex-Nter129"/>
        <expand macro="mod_option" value="TMT6plex-Nter130"/>
        <expand macro="mod_option" value="TMT6plex-Nter131"/>
        <expand macro="mod_option" value="TMT8plex-Nter126C"/>
        <expand macro="mod_option" value="TMT8plex-Nter127N"/>
        <expand macro="mod_option" value="TMT8plex-Nter127C"/>
        <expand macro="mod_option" value="TMT8plex-Nter128C"/>
        <expand macro="mod_option" value="TMT8plex-Nter129N"/>
        <expand macro="mod_option" value="TMT8plex-Nter129C"/>
        <expand macro="mod_option" value="TMT8plex-Nter130C"/>
        <expand macro="mod_option" value="TMT8plex-Nter131N"/>
        <expand macro="mod_option" value="TMT10plex-Nter126C"/>
        <expand macro="mod_option" value="TMT10plex-Nter127N"/>
        <expand macro="mod_option" value="TMT10plex-Nter127C"/>
        <expand macro="mod_option" value="TMT10plex-Nter128N"/>
        <expand macro="mod_option" value="TMT10plex-Nter128C"/>
        <expand macro="mod_option" value="TMT10plex-Nter129N"/>
        <expand macro="mod_option" value="TMT10plex-Nter129C"/>
        <expand macro="mod_option" value="TMT10plex-Nter130N"/>
        <expand macro="mod_option" value="TMT10plex-Nter130C"/>
        <expand macro="mod_option" value="TMT10plex-Nter131N"/>
        <expand macro="mod_option" value="TMT11plex-Nter131C"/>
        <expand macro="mod_option" value="TMT6plex-Lys126"/>
        <expand macro="mod_option" value="TMT6plex-Lys127"/>
        <expand macro="mod_option" value="TMT6plex-Lys128"/>
        <expand macro="mod_option" value="TMT6plex-Lys129"/>
        <expand macro="mod_option" value="TMT6plex-Lys130"/>
        <expand macro="mod_option" value="TMT6plex-Lys131"/>
        <expand macro="mod_option" value="TMT8plex-Lys126C"/>
        <expand macro="mod_option" value="TMT8plex-Lys127N"/>
        <expand macro="mod_option" value="TMT8plex-Lys127C"/>
        <expand macro="mod_option" value="TMT8plex-Lys128C"/>
        <expand macro="mod_option" value="TMT8plex-Lys129N"/>
        <expand macro="mod_option" value="TMT8plex-Lys129C"/>
        <expand macro="mod_option" value="TMT8plex-Lys130C"/>
        <expand macro="mod_option" value="TMT8plex-Lys131N"/>
        <expand macro="mod_option" value="TMT10plex-Lys126C"/>
        <expand macro="mod_option" value="TMT10plex-Lys127N"/>
        <expand macro="mod_option" value="TMT10plex-Lys127C"/>
        <expand macro="mod_option" value="TMT10plex-Lys128N"/>
        <expand macro="mod_option" value="TMT10plex-Lys128C"/>
        <expand macro="mod_option" value="TMT10plex-Lys129N"/>
        <expand macro="mod_option" value="TMT10plex-Lys129C"/>
        <expand macro="mod_option" value="TMT10plex-Lys130N"/>
        <expand macro="mod_option" value="TMT10plex-Lys130C"/>
        <expand macro="mod_option" value="TMT10plex-Lys131N"/>
        <expand macro="mod_option" value="TMT11plex-Lys131C"/>
        <expand macro="mod_option" value="iodoTMT6plex-Cys126"/>
        <expand macro="mod_option" value="iodoTMT6plex-Cys127"/>
        <expand macro="mod_option" value="iodoTMT6plex-Cys128"/>
        <expand macro="mod_option" value="iodoTMT6plex-Cys129"/>
        <expand macro="mod_option" value="iodoTMT6plex-Cys130"/>
        <expand macro="mod_option" value="iodoTMT6plex-Cys131"/>
    </xml>

    <xml name="citations">        
        <citations>
            <citation type="bibtex">
                @article{cox2008maxquant,
                title={MaxQuant enables high peptide identification rates, individualized
                ppb-range mass accuracies and proteome-wide protein quantification},
                author={Cox, J{\"u}rgen and Mann, Matthias},
                journal={Nature biotechnology},
                volume={26},
                number={12},
                pages={1367},
                year={2008},
                publisher={Nature Publishing Group}
                }
            </citation>
            <citation type="bibtex">
                @article{tyanova2016maxquant,
                title={The MaxQuant computational platform for mass
                spectrometry-based shotgun proteomics},
                author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
                journal={Nature protocols},
                volume={11},
                number={12},
                pages={2301},
                year={2016},
                publisher={Nature Publishing Group}
                }
            </citation>
            <citation type="doi">10.1021/acs.jproteome.5b00780</citation>
        </citations>
    </xml>
</macros>