Mercurial > repos > galaxyp > maxquant
diff maxquant.xml @ 0:4ce8694766e3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
| author | galaxyp |
|---|---|
| date | Fri, 19 Jul 2019 19:13:15 -0400 |
| parents | |
| children | 33c911e66d8e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant.xml Fri Jul 19 19:13:15 2019 -0400 @@ -0,0 +1,364 @@ +<tool id="maxquant" name="MaxQuant" version="@VERSION@"> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">maxquant</requirement> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #import re + + python3 '$__tool_directory__/mqwrapper.py' + --num_threads=\${GALAXY_SLOTS:-1} + --substitution_rx='@SUBSTITUTION_RX@' + #if $input_opts.infile.select == "mzxml_files" + --mzxml_files='$input_opts.infile.mzxml_files' + #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.mzxml_files]) + #else + --raw_files='$input_opts.infile.raw_files' + #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.raw_files]) + #end if + --infile_names='$names' + --version='@VERSION@' + --fasta_files='$input_opts.fasta_files' + --identifier_parse_rule='$input_opts.identifier_parse_rule' + --description_parse_rule='$input_opts.description_parse_rule' + + --exp_design='$search_opts.template' + --missed_cleavages=$search_opts.missed_cleavages + --min_peptide_len=$search_opts.min_peptide_len + --max_peptide_mass=$search_opts.max_peptide_mass + --min_unique_pep=$search_opts.min_unique_pep + $search_opts.calc_peak_properties + $search_opts.match_between_runs + #if $search_opts.fixed_mods + --fixed_mods='$search_opts.fixed_mods' + #end if + #if $search_opts.var_mods + --var_mods='$search_opts.var_mods' + #end if + #if $search_opts.proteases + --proteases='$search_opts.proteases' + #end if + #if $search_opts.silac.light_mods + --light_mods='$search_opts.silac.light_mods' + #end if + #if $search_opts.silac.medium_mods + --medium_mods='$search_opts.silac.medium_mods' + #end if + #if $search_opts.silac.heavy_mods + --heavy_mods='$search_opts.silac.heavy_mods' + #end if + #if $search_opts.lfq.do_lfq == "--lfq_mode=1" + $search_opts.lfq.do_lfq.lfq_mode + --lfq_min_ratio_count=$search_opts.lfq.do_lfq.lfq_min_ratio_count + --lfq_min_edges_per_node=$search_opts.lfq.do_lfq.lfq_min_edges_per_node + --lfq_avg_edges_per_node=$search_opts.lfq.do_lfq.lfq_avg_edges_per_node + $search_opts.lfq.do_lfq.lfq_skip_norm + $search_opts.lfq.do_lfq.separate_lfq + $search_opts.lfq.do_lfq.lfq_stabilize_large_ratios + $search_opts.lfq.do_lfq.lfq_require_msms + #if $search_opts.lfq.do_lfq.do_ibaq == "--ibaq" + $search_opts.lfq.do_lfq.do_ibaq.ibaq + $search_opts.lfq.do_lfq.do_ibaq.ibaq_log_fit + #end if + $search_opts.lfq.do_lfq.advanced_site_intensities + #end if + + $output_opts.write_mztab + --evidence='$evidence' + --msms='$msms' + --parameters='$parameters' + --peptides='$peptides' + --proteinGroups='$proteinGroups' + --allPeptides='$allPeptides' + --libraryMatch='$libraryMatch' + --matchedFeatures='$matchedFeatures' + --modificationSpecificPeptides='$modificationSpecificPeptides' + --ms3Scans='$ms3Scans' + --msmsScans='$msmsScans' + --mzRange='$mzRange' + --peptideSection='$peptideSection' + --summary='$summary' + --mzTab='$mzTab' + --mqpar_out='$mqpar_out' + + #if 'log' in $output_opts.output + > '$log' + #end if + #if 'output_all' in $output_opts.output + && tar -zcf '$output_all' ./combined/txt + #end if + ]]></command> + <inputs> + <section name="input_opts" title="Input Options" expanded="True"> + <conditional name="infile"> + <param name="select" type="select" label="choose the type of your input files"> + <option value="raw_files">Thermo.raw</option> + <option value="mzxml_files">mzXML</option> + </param> + <when value="raw_files"> + <param multiple="true" name="raw_files" type="data" + format="thermo.raw" label="RAW Files" + help="Specify one or more Thermo RAW files" /> + </when> + <when value="mzxml_files"> + <param multiple="true" name="mzxml_files" type="data" + format="mzxml" label="mzXML Files" + help="Specify one or more mzXML files" /> + </when> + </conditional> + <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="^>.*\|(.*)\|.*$"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param name="description_parse_rule" type="text" + label="description parse rule" value="^>.*\|.*\|[^ ]+ (.*) OS.*$" + help="Modify parse rules if needed"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </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="missed_cleavages" + label="missed cleavages" value="1"/> + <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="1" /> + <param name="calc_peak_properties" type="boolean" checked="false" + label="Calculate peak properties?" + truevalue="--calc_peak_properties" falsevalue="" /> + <param name="match_between_runs" type="boolean" checked="false" + label="Match between runs?" + truevalue="--match_between_runs" falsevalue="" /> + <param name="fixed_mods" type="select" label="fixed modifications" + multiple="true" help="select zero or more fixed modifications"> + <expand macro="modification"/> + </param> + <param name="var_mods" type="select" label="variable modifications" + multiple="true" help="select zero or more variable modifications"> + <expand macro="modification"/> + </param> + <param name="proteases" type="select" label="proteases" + multiple="true" help="select zero or more proteases"> + <expand macro="proteases"/> + </param> + <section title="label based quantitation" name="silac" expanded="false"> + <param name="light_mods" type="select" label="light labels" + multiple="true" help="select zero or more light modifications"> + <expand macro="label"/> + </param> + <param name="medium_mods" type="select" label="medium labels" + multiple="true" help="select zero or more medium modifications"> + <expand macro="label"/> + </param> + <param name="heavy_mods" type="select" label="heavy labels" + multiple="true" help="select zero or more heavy modifications"> + <expand macro="label"/> + </param> + </section> + <section title="label free quantification" name="lfq" expanded="false"> + <conditional name="do_lfq"> + <param name="lfq_mode" type="select" label="Perform LFQ?"> + <option value="">No</option> + <option value="--lfq_mode=1">Yes</option> + </param> + <when value="--lfq_mode=1"> + <param type="integer" name="lfq_min_ratio_count" + label="LFQ minimum ratio count" value="2"/> + <param type="integer" name="lfq_min_edges_per_node" + label="LFQ minimum number of neighbours" value="3"/> + <param type="integer" name="lfq_avg_edges_per_node" + label="LFQ average number of neighbours" value="6"/> + <param name="lfq_skip_norm" type="boolean" checked="false" + label="Skip normalization?" + truevalue="--lfq_skip_norm" falsevalue="" /> + <param name="separate_lfq" type="boolean" checked="false" + label="Separate LFQ in parameter Groups?" + truevalue="--separate_lfq" falsevalue="" /> + <param name="lfq_stabilize_large_ratios" type="boolean" checked="true" + label="Stabilize large LFQ ratios?" + truevalue="--lfq_stabilize_large_ratios" falsevalue="" /> + <param name="lfq_require_msms" type="boolean" checked="true" + label="Require MS/MS for LFQ comparisons?" + truevalue="--lfq_require_msms" falsevalue="" /> + <conditional name="do_ibaq"> + <param name="ibaq" type="select" label="iBAQ?"> + <option value="">No</option> + <option value="--ibaq">Yes</option> + </param> + <when value="--ibaq"> + <param name="ibaq_log_fit" type="boolean" checked="true" + label="Logarithmic fit?" + truevalue="--ibaq_log_fit" falsevalue="" /> + </when> + <when value=""> + </when> + </conditional> + <param name="advanced_site_intensities" type="boolean" checked="true" + label="Advanced site intensities?" + truevalue="--advanced_site_intensities" falsevalue="" /> + </when> + <when value=""> + </when> + </conditional> + </section> + </section> + + <section title="Output Options" name="output_opts" expanded="true"> + <param name="write_mztab" type="boolean" checked="false" + label="Write mztab file?" + truevalue="--write_mztab" falsevalue="" /> + <param type="select" name="output" label="Select the desired outputs." + multiple="true" optional="false"> + <expand macro="output_option" name="proteinGroups" label="Protein Groups"/> + <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/> + <expand macro="output_option" name="peptides" label="Peptides"/> + <expand macro="output_option" name="evidence" label="Evidence"/> + <expand macro="output_option" name="parameters" label="Tabular Paramters"/> + <expand macro="output_option" name="msms" label="MSMS"/> + <expand macro="output_option" name="mzTab" label="mzTab"/> + <expand macro="output_option" name="allPeptides" label="all peptides"/> + <expand macro="output_option" name="libraryMatch" label="library match"/> + <expand macro="output_option" name="matchedFeatures" label="matched features"/> + <expand macro="output_option" name="modificationSpecificPeptides" label="modification specific peptides"/> + <expand macro="output_option" name="ms3Scans" label="ms3 scans"/> + <expand macro="output_option" name="msmsScans" label="msms scans"/> + <expand macro="output_option" name="mzRange" label="mz range"/> + <expand macro="output_option" name="peptideSection" label="peptide section"/> + <expand macro="output_option" name="summary" label="summary"/> + <expand macro="output_option" name="output_all" label="complete 'combined/txt/' directory (compressed)"/> + <expand macro="output_option" name="log" label="MaxQuant log"/> + </param> + </section> + </inputs> + + <outputs> + <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/> + <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/> + <expand macro="output" name="peptides" label="MaxQuant Peptides"/> + <expand macro="output" name="evidence" label="MaxQuant Evidence"/> + <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/> + <expand macro="output" name="msms" label="MaxQuant MSMS"/> + <expand macro="output" name="mzTab" label="mzTab"/> + <expand macro="output" name="allPeptides" label="all peptides"/> + <expand macro="output" name="libraryMatch" label="library match"/> + <expand macro="output" name="matchedFeatures" label="matched features"/> + <expand macro="output" name="modificationSpecificPeptides" label="modification specific peptides"/> + <expand macro="output" name="ms3Scans" label="ms3 scans"/> + <expand macro="output" name="msmsScans" label="msms Scans"/> + <expand macro="output" name="mzRange" label="mz range"/> + <expand macro="output" name="peptideSection" label="peptide section"/> + <expand macro="output" name="summary" label="MaxQuant summary"/> + <expand macro="output" format="tar" name="output_all" label="'combined/txt/' directory"/> + <expand macro="output" name="log" format="txt" label="log"/> + </outputs> + + <tests> + <test> + <param name="select" value="mzxml_files" /> + <param name="mzxml_files" value="BSA_min_23.mzXML" /> + <param name="fasta_files" value="bsa.fasta" /> + <param name="identifier_parse_rule" value=">([^\s]*)" /> + <param name="description_parse_rule" value=">(.*)" /> + <param name="min_unique_pep" value="0" /> + <param name="fixed_mods" value="Carbamidomethyl (C)" /> + <param name="var_mods" value="Oxidation (M)" /> + <param name="proteases" value="Trypsin/P" /> + <param name="write_mztab" value="true" /> + <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" /> + <output name="evidence" file="single/combined/txt/evidence.txt" /> + <output name="msms" file="single/combined/txt/msms.txt" /> + <output name="mzTab" file="single/combined/txt/mzTab.mzTab" lines_diff="4"/> + <output name="allPeptides" file="single/combined/txt/allPeptides.txt" /> + <output name="msmsScans" file="single/combined/txt/msmsScans.txt" /> + <output name="mzRange" file="single/combined/txt/mzRange.txt" /> + <output name="parameters" file="single/combined/txt/parameters.txt" lines_diff="10"/> + <output name="peptides" file="single/combined/txt/peptides.txt" /> + <output name="peptideSection" file="single/combined/txt/peptideSection.txt" /> + <output name="proteinGroups" file="single/combined/txt/proteinGroups.txt" /> + <output name="summary" file="single/combined/txt/summary.txt" /> + <output name="modificationSpecificPeptides" file="single/combined/txt/modificationSpecificPeptides.txt" /> + </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 file or mzXML file + - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes) +- 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 Fraction are abitrary strings, Experiment is an integer, PTM is either True or False. + + :: + + Name Fraction Experiment PTM + File1 1 E1 False + File2 2 E1 False + File3 3 E1 False + ... + ... + +**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 + +**Output files** + +Different output file options are available, most of them are part of the MaxQuant txt directory. + ]]></help> + <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> + </citations> +</tool>