Mercurial > repos > galaxyp > maxquant_mqpar
diff maxquant_mqpar.xml @ 3:2d67fb758956 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
| author | galaxyp |
|---|---|
| date | Sat, 11 Apr 2020 11:50:09 -0400 |
| parents | 3fc2116ac6d9 |
| children | 9cb7dcc07dae |
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--- a/maxquant_mqpar.xml Thu Aug 15 08:09:38 2019 -0400 +++ b/maxquant_mqpar.xml Sat Apr 11 11:50:09 2020 -0400 @@ -1,67 +1,86 @@ <tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" 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</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 ${on_string}" name="@NAME@"> + <filter>'@NAME@' in output</filter> + </data> + </xml> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="@VERSION@">maxquant</requirement> - <requirement type="package" version="3.7">python</requirement> - </requirements> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ + ## link galaxy datasets to filenames accepted by maxquant #import re + #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input.infiles] + #set names_with_ext = [($name if ($name).lower().endswith(str($input.ftype)) else $name + str($input.ftype)) for $name in $names] + #for $target, $link in zip($infiles, $names_with_ext) + ln -s '$target' '$link' && + #end for - python3 '$__tool_directory__/mqwrapper.py' + python3 '$__tool_directory__/modify_mqpar.py' + #set inf = ','.join($names_with_ext) + --infiles='$inf' + --version=@VERSION@ --num_threads=\${GALAXY_SLOTS:-1} --substitution_rx='@SUBSTITUTION_RX@' - #if $infile.select == "mzxml_files" - --mzxml_files='$infile.mzxml_files' - #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.mzxml_files]) - #else - --raw_files='$infile.raw_files' - #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $infile.raw_files]) - #end if - --infile_names='$names' - --version='@VERSION@' --fasta_files='$fasta_files' + --description_parse_rule='$description_parse_rule' --identifier_parse_rule='$identifier_parse_rule' - --description_parse_rule='$description_parse_rule' - --mqpar_in='$mqpar_in' + '$mqpar' - --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='$mzTab' - --output_all='$output_all' - --mqpar_out='$mqpar_out' + && + maxquant mqpar.xml + #if 'log' in $output: + >> '$log' + #end if + && mv '$mqpar' combined/txt/mqpar.xml + #if 'output_all' in $output: + && + tar -zcf '$output_all' ./combined/txt + #end if + + #if $qc.do_it: + && + Rscript '$qr' '$qr_yaml' + #if 'log' in $output: + >> '$log' 2>&1 + #end if + && + cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report' + #end if + ]]></command> - > '$log' - ]]></command> + <configfiles> + <expand macro="ptxqc"/> + </configfiles> + <inputs> - <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> + <conditional name="input"> + <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> - <when value="raw_files"> - <param multiple="true" name="raw_files" type="data" + <when value=".thermo.raw"> + <param multiple="true" name="infiles" 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" + <when value=".mzxml"> + <param multiple="true" name="infiles" type="data" + format="mzXML" label="mzXML Files" help="Specify one or more mzXML files" /> </when> + <when value=".mzml"> + <param multiple="true" name="infiles" type="data" + format="mzML" label="mzML Files" + help="Specify one or more mzML files" /> + </when> </conditional> <param format="fasta" multiple="true" name="fasta_files" type="data" label="FASTA files" @@ -83,93 +102,63 @@ </valid> </sanitizer> </param> - <param type="data" name="mqpar_in" format="xml" + <param type="data" name="mqpar" format="xml" label="mqpar.xml file with your search parameters. RAW file names must match the names displayed in galaxy. Their paths from the local machine are ignored. E.g. a file named 'test01.raw' in galaxy can either be named 'test01.raw' or 'D:\path\to\test01.raw' in the mqpar.xml."/> - + <expand macro="ptxqc-opts"/> <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)"/> + <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> </param> </inputs> - <outputs> - <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/> - <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/> - <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"/> - <data name="log" format="txt" - label="log"/> - </outputs> + <expand macro="outputs"/> <tests> <test> - <param name="select" value="mzxml_files" /> - <param name="mzxml_files" value="BSA_min_22,BSA_min_21.mzXML" /> + <param name="ftype" value=".mzxml" /> + <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" /> <param name="fasta_files" value="bsa.fasta" /> <param name="identifier_parse_rule" value=">([^\s]*)" /> <param name="description_parse_rule" value=">(.*)" /> - <param name="mqpar_in" value="two/mqpar.xml" /> - <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" /> - <output name="evidence" file="two/combined/txt/evidence.txt" /> - <output name="msms" file="two/combined/txt/msms.txt" /> - <output name="mzTab" file="two/combined/txt/mzTab.mzTab" lines_diff="4"/> - <output name="allPeptides" file="two/combined/txt/allPeptides.txt" lines_diff="14"/> - <output name="msmsScans" file="two/combined/txt/msmsScans.txt" /> - <output name="mzRange" file="two/combined/txt/mzRange.txt" /> - <output name="parameters" file="two/combined/txt/parameters.txt" lines_diff="8"/> - <output name="peptides" file="two/combined/txt/peptides.txt" /> - <output name="peptideSection" file="two/combined/txt/peptideSection.txt" /> - <output name="proteinGroups" file="two/combined/txt/proteinGroups.txt" /> - <output name="summary" file="two/combined/txt/summary.txt" /> - <output name="modificationSpecificPeptides" file="two/combined/txt/modificationSpecificPeptides.txt" /> + <param name="mqpar" value="mqpar.xml" /> + <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all" /> + <output name="evidence" file="txt/evidence.txt" /> + <output name="msms" file="txt/msms.txt" lines_diff="2" /> + <output name="allPeptides" file="txt/allPeptides.txt" lines_diff="32" /> + <output name="msmsScans" file="txt/msmsScans.txt" lines_diff="4"/> + <output name="mzRange" file="txt/mzRange.txt" /> + <output name="parameters" file="txt/parameters.txt" lines_diff="8"/> + <output name="peptides" file="txt/peptides.txt" /> + <output name="proteinGroups" file="txt/proteinGroups.txt" /> + <output name="summary" file="txt/summary.txt" /> + <output name="modificationSpecificPeptides" file="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@. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred. +This tool is a wrapper for MaxQuant v@VERSION@. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred, if possible. **Input files** @@ -182,32 +171,5 @@ Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented. ]]></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> + <expand macro="citations"/> </tool>