Mercurial > repos > galaxyp > maxquant
diff macros.xml @ 4:dcd39bcc7481 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
| author | galaxyp |
|---|---|
| date | Sat, 11 Apr 2020 11:49:19 -0400 |
| parents | 8bac3cc5c5de |
| children | 7f432d87c82c |
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--- a/macros.xml Thu Aug 15 08:09:00 2019 -0400 +++ b/macros.xml Sat Apr 11 11:49:19 2020 -0400 @@ -1,18 +1,185 @@ <?xml version="1.0" ?> <macros> - <token name="@VERSION@">1.6.3.4</token> + <token name="@VERSION@">1.6.10.43</token> <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> - <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> + <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="output_option" token_label="default label" token_name="default"> - <option value="@NAME@">@LABEL@</option> + + <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? (at own risk)" + 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)"/> @@ -430,6 +597,7 @@ <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"/> @@ -466,6 +634,7 @@ <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"/> @@ -481,5 +650,123 @@ <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> -