annotate maxquant.xml @ 4:dcd39bcc7481 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"

<tool id="maxquant" name="MaxQuant" version="@VERSION@">
    <macros>
        <xml name="output" token_format="tabular" token_label="default description" token_name="default">
            <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
                <filter>'@NAME@' in output_opts['output']</filter>
            </data>
        </xml>
        <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">
            <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
                <filter>'@NAME@' in output_opts['output']</filter>
            </data>
        </xml>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    #import re
    maxquant -c mqpar.xml 2>/dev/null  ## MQ writes success of creation to stderr
    #if 'config' in $output_opts.output:
      &&
      cp '$mq_conf' '$config'
    #end if
    #set infiles = [$name for $pg in $paramGroups for $name in $pg.files]
    #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $infiles]
    #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
    #for $target, $link in zip($infiles, $names_with_ext)
        &&
        ln -s '$target' '$link'
    #end for
    &&
    python3 '$__tool_directory__/create_mqpar.py'
    #if $search_opts.template
        --exp_design='$search_opts.template'
    #end if
    --version=@VERSION@ 
    --num_threads=\${GALAXY_SLOTS:-1}
    --substitution_rx='@SUBSTITUTION_RX@'
    --yaml='$mq_conf'
    mqpar.xml

    #if $output_opts.dry_run:
      &&
      mkdir -p combined/txt
      &&
      mv mqpar.xml combined/txt/mqpar.xml
    #else:
      && 
      maxquant mqpar.xml
      #if 'log' in $output_opts.output:
          > '$log'
      #end if
      &&
      mv mqpar.xml combined/txt/mqpar.xml
      #if 'output_all' in $output_opts.output:
          &&
          tar -zcf '$output_all' ./combined/txt
      #end if
      
      #if $qc.do_it:
        &&
        Rscript '$qr' '$qr_yaml'
          #if 'log' in $output_opts.output:
              >> '$log' 2>&1
          #end if
        &&
        cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report'
      #end if
    #end if
    ]]></command>

    <configfiles>
        <configfile name="mq_conf">
            #import re
            fastaFiles: [${input_opts.fasta_files}]
            parseRules:
              identifierParseRule: '${input_opts.identifier_parse_rule}'
              descriptionParseRule: '${input_opts.description_parse_rule}'
            minUniquePeptides: ${search_opts.min_unique_pep}
            minPepLen: ${search_opts.min_peptide_len}
            maxPeptideMass: ${search_opts.max_peptide_mass}
            calcPeakProperties: ${search_opts.calc_peak_properties}
            #set writeMzTab = "mzTab" in $output_opts.output
            writeMzTab: $writeMzTab
            #if $lfq_opts.do_ibaq.ibaq == 'True':
            ibaq: ${lfq_opts.do_ibaq.ibaq}
            ibaqLogFit: ${lfq_opts.do_ibaq.ibaqLogFit}
            #end if
            separateLfq: ${lfq_opts.separateLfq}
            lfqStabilizeLargeRatios: ${lfq_opts.lfqStabilizeLargeRatios}
            lfqRequireMsms: ${lfq_opts.lfqRequireMsms}
            advancedSiteIntensities: ${lfq_opts.advancedSiteIntensities}
            matchBetweenRuns: ${search_opts.match_between_runs}
            paramGroups:
            #for $pg in $paramGroups:
              #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $pg.files]
              #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
              - files: $names_with_ext
                maxMissedCleavages: ${pg.maxMissedCleavages}
                #if $pg.fixedModifications:
                fixedModifications: [${pg.fixedModifications}]
                #else:
                fixedModifications: []
                #end if
                #if $pg.variableModifications:
                variableModifications: [${pg.variableModifications}]
                #else:
                variableModifications: []
                #end if
                #if $pg.enzymes:
                enzymes: [${pg.enzymes}]
                #else:
                enzymes: []
                #end if
                #if $pg.quant_method.select_quant_method == 'silac':
                labelMods:
                  #if $pg.quant_method.light_labels:
                  - [${pg.quant_method.light_labels}]
                  #else:
                  - []
                  #end if
                  #if $pg.quant_method.medium_labels:
                  - [${pg.quant_method.medium_labels}]
                  #else:
                  - []
                  #end if
                  #if $pg.quant_method.heavy_labels:
                  - [${pg.quant_method.heavy_labels}]
                  #else:
                  - []
                  #end if
                #end if
                #if $pg.quant_method.select_quant_method == 'lfq':
                lfqMode: 1
                lfqSkipNorm: ${pg.quant_method.lfqSkipNorm}
                lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode}
                lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode}
                lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
                #end if
                #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
                lcmsRunType: 'Reporter ion MS2'
                reporterMassTolerance: 0.003
                reporterPif: 0
                reporterFraction: 0
                reporterBasePeakRatio: 0
                isobaricLabels:
                  #if $pg.quant_method.iso_labels.labeling == 'custom':
                    #for $l in $pg.quant_method.iso_labels.iso_label:
                      - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
                    #end for
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
                    - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
                    - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
                    - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]
                    - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
                    - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
                    - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
                    - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
                    - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
                    - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]
                    - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
                    - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
                    - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
                    - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
                    - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
                    - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
                    - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
                    @TMT10PLEX@
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
                    @TMT10PLEX@
                    - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
                    - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
                    - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
                    - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
                    - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
                    - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]
                    - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False]
                    - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False]
                    - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False]
                    - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False]
                    - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
                    - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
                    - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
                  #end if
                  #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
                    - [iodoTMT6plex-Cys126,'',0,0,0,0,True]
                    - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
                    - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
                    - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
                    - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
                    - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
                  #end if
                #end if  
            #end for
        </configfile>
        <expand macro="ptxqc"/>
    </configfiles>

    <inputs>
        <section name="input_opts" title="Input Options" expanded="True">
            <param name="ftype" type="select" label="choose the type of your input files">
                <option value=".thermo.raw">thermo.raw</option>
                <option value=".mzxml">mzxml</option>
                <option value=".mzml">mzml</option>
            </param>
            <param format="fasta" multiple="true" name="fasta_files"
                   type="data" label="FASTA files"
                   help="Specify one or more FASTA databases." />
            <param name="identifier_parse_rule" type="text"
                   label="identifier parse rule" value="^&gt;.*\|(.*)\|.*$">
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="description_parse_rule" type="text"
                   label="description parse rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$"
                   help="Modify parse rules if needed">
                <sanitizer>
                    <valid initial="string.printable">
                        <remove value="&apos;"/>
                    </valid>
                </sanitizer>
            </param>
        </section>

        <section name="search_opts" title="Search Options" expanded="true">
            <param format="tabular" name="template" type="data" optional="true"
                   label="Specify an experimental design template (if needed). For detailed
                          instructions see the help text." />
            <param type="integer" name="min_peptide_len"
	           label="minimum peptide length" value="7"/>
            <param type="integer" name="max_peptide_mass"
	           label="maximum peptide mass" value="4600"/>
            <param type="integer" name="min_unique_pep"
	           label="minimum unique peptides" value="0" />
            <param name="calc_peak_properties" type="boolean" checked="false"
	           label="Calculate peak properties?"
	           truevalue="True" falsevalue="False" />
            <param name="match_between_runs" type="boolean" checked="false"
	           label="Match between runs?"
	           truevalue="True" falsevalue="False" />
        </section>
        
        <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
            <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true"
                   help="Only select infiles matching the filetype specified in the input options."/>
            <param type="integer" name="maxMissedCleavages"
	           label="missed cleavages" value="2"/>
            <param name="fixedModifications" type="select" label="fixed modifications"
	           multiple="true" help="select zero or more fixed modifications">
	        <expand macro="modification"/>
                <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
            </param>
            <param name="variableModifications" type="select" label="variable modifications"
	           multiple="true" help="select zero or more variable modifications">
                <expand macro="default_mod_option" value="Oxidation (M)"/>
                <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
	        <expand macro="modification"/>
            </param>
            <param name="enzymes" type="select" label="proteases"
	           multiple="true" help="select zero or more proteases">
                <expand macro="default_mod_option" value="Trypsin/P"/>
	        <expand macro="proteases"/>
            </param>
            <conditional name="quant_method">
                <param name="select_quant_method" type="select" label="Quantitation Methods"
                       help="Select a method if needed.">
                    <option value="">None</option>
                    <option value="lfq">label free quantification</option>
                    <option value="silac">label based quantification (SILAC)</option>
                    <option value="reporter_ion_ms2">reporter ion MS2</option>
                </param>
                <when value=""/>
                <when value="silac">
	            <param name="light_labels" type="select" label="light labels"
		           multiple="true" help="select zero or more light modifications">
	                <expand macro="label"/>
	            </param>
	            <param name="medium_labels" type="select" label="medium labels"
		           multiple="true" help="select zero or more medium modifications">
	                <expand macro="label"/>
	            </param>
	            <param name="heavy_labels" type="select" label="heavy labels"
		           multiple="true" help="select zero or more heavy modifications">
	                <expand macro="label"/>
	            </param>
                </when>
                <when value="lfq">
		    <param type="integer" name="lfqMinRatioCount"
		           label="LFQ minimum ratio count" value="2"/>
		    <param type="integer" name="lfqMinEdgesPerNode"
			   label="LFQ minimum number of neighbours" value="3"/>
		    <param type="integer" name="lfqAvEdgesPerNode"
			   label="LFQ average number of neighbours" value="6"/>
		    <param type="boolean" name="lfqSkipNorm" checked="true"
			   label="Skip normalization?"
			   truevalue="True" falsevalue="False" />
                </when>
                <when value="reporter_ion_ms2">
                    <conditional name="iso_labels">
                        <param name="labeling" type="select" label="isobaric labeling"
                               help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
                            <option value="custom">custom</option>
                            <option value="tmt2plex">TMT2plex</option>
                            <option value="tmt6plex">TMT6plex</option>
                            <option value="tmt8plex">TMT8plex</option>
                            <option value="tmt10plex">TMT10plex</option>
                            <option value="tmt11plex">TMT11plex</option>
                            <option value="itraq4plex">iTRAQ4plex</option>
                            <option value="itraq8plex">iTRAQ8plex</option>
                            <option value="iodotmt6plex">iodoTMT6plex</option>
                        </param>
                        <when value="tmt2plex"></when>
                        <when value="tmt6plex"></when>
                        <when value="tmt8plex"></when>
                        <when value="tmt10plex"></when>
                        <when value="tmt11plex"></when>
                        <when value="itraq4plex"></when>
                        <when value="itraq8plex"></when>
                        <when value="iodotmt6plex"></when>
                        <when value="custom">
                            <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
                                <param name="internallabel" type="select" label="internal label">
	                            <expand macro="iso_labels"/>
	                        </param>
                                <param name="terminallabel" type="select" label="terminal label">
                                    <option value="">None</option>
	                            <expand macro="iso_labels"/>
	                        </param>
                                <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
                                <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
                                <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
                                <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
		                <param type="boolean" name="tmtlike" checked="false"
			               label="TMT-like"
			               truevalue="True" falsevalue="False" />
                            </repeat>
                        </when>
                    </conditional>
                </when>
            </conditional>
        </repeat>

        <section title="LFQ Options" name="lfq_opts" expanded="false">
	    <param name="separateLfq" type="boolean" checked="false"
		   label="Separate LFQ in parameter Groups?"
		   truevalue="True" falsevalue="False" />
	    <param name="lfqStabilizeLargeRatios" type="boolean" checked="true"
		   label="Stabilize large LFQ ratios?"
		   truevalue="True" falsevalue="False" />
	    <param name="lfqRequireMsms" type="boolean" checked="true"
		   label="Require MS/MS for LFQ comparisons?"
		   truevalue="True" falsevalue="False" />
	    <conditional name="do_ibaq">
                <param name="ibaq" type="select" label="iBAQ?">
                    <option value="False">No</option>
                    <option value="True">Yes</option>
		</param>
                <when value="True">
                    <param name="ibaqLogFit" type="boolean" checked="true"
                           label="Logarithmic fit?"
                           truevalue="True" falsevalue="False" />
                </when>
                <when value="False">
                </when>
	    </conditional>
	    <param name="advancedSiteIntensities" type="boolean" checked="true"
		   label="Advanced site intensities?"
		   truevalue="True" falsevalue="False" />
        </section>

        <expand macro="ptxqc-opts"/>
        <section title="Output Options" name="output_opts" expanded="true">
            <param name="dry_run" type="boolean" checked="false"
	           label="Only create config files? (i.e. for testing)"
	           truevalue="True" falsevalue="" />            
            <param type="select" name="output" label="Select the desired outputs."
                   multiple="true" optional="false">
                <option value="proteinGroups">Protein Groups</option>
                <option value="mqpar">mqpar.xml</option>
                <option value="peptides">Peptides</option>
                <option value="evidence">Evidence</option>
                <option value="parameters">Tabular Paramters</option>
                <option value="msms">MSMS</option>
                <option value="mzTab">mzTab</option>
                <option value="allPeptides">all peptides</option>
                <option value="libraryMatch">library match</option>
                <option value="matchedFeatures">matched features</option>
                <option value="modificationSpecificPeptides">modification specific peptides</option>
                <option value="ms3Scans">ms3 scans</option>
                <option value="msmsScans">msms scans</option>
                <option value="mzRange">mz range</option>
                <option value="peptideSection">peptide section</option>
                <option value="summary">summary</option>
                <option value="output_all">complete 'combined/txt/' directory (compressed)</option>
                <option value="log">MaxQuant and PTXQC log</option>
                <option value="config">yaml config file</option>
            </param>
        </section>
    </inputs>
    
    <expand macro="outputs"/>

    <tests>
        <!-- functional test with small mzXML file, no quantitation methods -->
        <test expect_num_outputs="15">
            <param name="ftype" value=".mzxml" />
            <param name="fasta_files" value="bsa.fasta" />
            <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
            <param name="description_parse_rule" value="&gt;(.*)" />
            <repeat name="paramGroups">
                <param name="files" value="BSA_min_23.mzXML"/>
                <param name="maxMissedCleavages" value="1"/>
                <param name="fixedModifications" value="Carbamidomethyl (C)" />
                <param name="variableModifications" value="Oxidation (M)" />
                <param name="enzymes" value="Trypsin/P" />
            </repeat>
            <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all,config,mqpar" />
            <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/>
            <output name="evidence" file="01/combined/txt/evidence.txt" />
            <output name="msms" file="01/combined/txt/msms.txt" />
            <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="4"/>
            <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="4"/>
            <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/>
            <output name="mzRange" file="01/combined/txt/mzRange.txt" />
            <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/>
            <output name="peptides" file="01/combined/txt/peptides.txt" />
            <output name="peptideSection" file="01/combined/txt/peptideSection.txt" />
            <output name="proteinGroups" file="01/combined/txt/proteinGroups.txt" />
            <output name="summary" file="01/combined/txt/summary.txt" />
            <output name="modificationSpecificPeptides" file="01/combined/txt/modificationSpecificPeptides.txt" />
            <output name="config" file="01/config.yml" lines_diff="2"/>
        </test>
        <!-- reporter ion ms2 + multiple param groups, testing yaml conf file and mqpar.xml only -->
        <test expect_num_outputs="3">
            <param name="ftype" value=".mzxml" />
            <param name="fasta_files" value="bsa.fasta" />
            <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
            <param name="description_parse_rule" value="&gt;(.*)" />
            <repeat name="paramGroups">
                <param name="files" value="BSA_min_23.mzXML"/>
                <param name="variableModifications" value="Oxidation (M)" />
                <param name="fixedModifications" value="" />
                <conditional name="quant_method">
                    <param name="select_quant_method" value="reporter_ion_ms2" />
                    <conditional name="iso_labels">
                        <param name="labeling" value="custom" />
                        <repeat name="iso_label">
                            <param name="internallabel" value="TMT2plex-Lys126" />
                            <param name="terminallabel" value="TMT2plex-Nter126" />
                            <param name="tmtlike" value="True" />
                            <param name="cp1" value="6.7" />
                            <param name="cp2" value="3" />
                        </repeat>
                        <repeat name="iso_label">
                            <param name="internallabel" value="TMT2plex-Lys127" />
                            <param name="terminallabel" value="TMT2plex-Nter127" />
                            <param name="tmtlike" value="True" />
                        </repeat>
                    </conditional>
                </conditional>
            </repeat>
            <repeat name="paramGroups">
                <param name="files" value="BSA_min_22"/>
                <param name="variableModifications" value="" />
                <param name="fixedModifications" value="" />
                <param name="enzymes" value="" />
                <conditional name="quant_method">
                    <param name="select_quant_method" value="reporter_ion_ms2" />
                    <conditional name="iso_labels">
                        <param name="labeling" value="itraq4plex" />
                    </conditional>
                </conditional>
            </repeat>
            <param name="dry_run" value="True" />
            <param name="output" value="config,mqpar,mzTab" />
            <output name="config" file="02/config.yml" lines_diff="2" />
            <!-- high difference due to unconsistant xml formatting in MQ -->
            <output name="mqpar" file="02/mqpar.xml" lines_diff="24" />
        </test>
        <!-- lfq, testing yaml conf file and mqpar.xml only -->
        <test expect_num_outputs="2">
            <param name="ftype" value=".mzxml" />
            <param name="fasta_files" value="bsa.fasta" />
            <param name="min_unique_pep" value="1" />
            <param name="ibaq" value="True" />
            <param name="ibaqLogFit" value="False" />
            <repeat name="paramGroups">
                <param name="files" value="BSA_min_22"/>
                <param name="maxMissedCleavages" value="1"/>
                <param name="variableModifications" value="Oxidation (M)" />
                <conditional name="quant_method">
                    <param name="select_quant_method" value="lfq" />
                </conditional>
            </repeat>
            <param name="dry_run" value="True" />
            <param name="output" value="config,mqpar" />
            <output name="config" file="03/config.yml" lines_diff="2" />
            <output name="mqpar" file="03/mqpar.xml" lines_diff="10" />
        </test>
        <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only -->
        <test expect_num_outputs="2">
            <param name="ftype" value=".mzxml" />
            <param name="fasta_files" value="bsa.fasta" />
            <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
            <param name="description_parse_rule" value="&gt;(.*)" />
            <param name="template" value="04/exp_design" />
            <repeat name="paramGroups">
                <param name="files" value="BSA_min_23.mzXML,BSA_min_22"/>
                <param name="fixedModifications" value="Carbamidomethyl (C)" />
                <param name="variableModifications" value="Oxidation (M)" />
                <param name="enzymes" value="Trypsin/P" />
                <conditional name="quant_method">
                    <param name="select_quant_method" value="silac" />
                    <param name="light_labels" value="Arg6,Lys4" />
                    <param name="heavy_labels" value="Arg10,DimethLys8" />
                </conditional>
            </repeat>
            <param name="dry_run" value="True" />
            <param name="output" value="config,mqpar" />
            <output name="config" file="04/config.yml" lines_diff="2" />
            <output name="mqpar" file="04/mqpar.xml" lines_diff="12" />
        </test>
    </tests>

    <help><![CDATA[
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 

This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a very reduced set of search parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too. If possible, this tool should be preferred. 

**Input files**

- Thermo raw files or mzXML files (in parameter group section):
    - The datatype of all files has to be either 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
- Fasta files: specify parse rules accordingly, default rules are compatible with uniprot
- Optional files:
    - Tabular file with experimental design template:
        - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template:

                ::

                    Name     Fraction    Experiment   PTM
                    File1        1          E1       False
                    File2        2          E1       False
                    ghost       234        none
                    File3        3          E1       False
                    File4                   E2       true
                    File5                   E1

        - This is the counter-example with one error per line:

                ::

                    Name     Fraction    Experiment   PTM
                    File1       1           E1        no  (wrong PTM value)
                    File2.mzxml 1           E2            (filename with extension)
                    File3       f3          E1            (fraction not an integer)
                    File4       1                         (missing experiment)
                                                          (File5 misssing)

**Parameter Options**

- Quantification options
    - label based: 
        - for two channels: choose options from light and heavy sections, for three channels choose options from light, medium and heavy sections
    - label-free
    - reporter ion ms2: either use the pre-defined labelings with correction factors set to 0 or specify a custom labeling

**Output files**

Different output file options are available, most of them are part of the MaxQuant txt directory. If ptxqc report ist selected, a quality control report will be created.
    ]]></help>
    <expand macro="citations"/>
</tool>