Mercurial > repos > recetox > rmassbank
diff rmassbank.xml @ 0:0b28816c1c2c draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
author | recetox |
---|---|
date | Thu, 18 May 2023 13:01:04 +0000 |
parents | |
children | c1a9c990d4b0 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmassbank.xml Thu May 18 13:01:04 2023 +0000 @@ -0,0 +1,232 @@ +<tool id="rmassbank" name="RMassBank" version="@TOOL_VERSION@+galaxy2"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="2.4.1">openbabel</requirement> + <requirement type="package" version="3.0.0">bioconductor-rmassbank</requirement> + <requirement type="package" version="3.1.1">r-gplots</requirement> + <requirement type="package" version="3.0">zip</requirement> + </requirements> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + </stdio> + <command detect_errors="aggressive"><![CDATA[ + #for $infile in $param_in: + ln -s '${infile}' '${infile.element_identifier}' && + #end for + + ln -s '${compounds}' '${compounds.element_identifier}' && + + mkdir -p ./infolists && + ln -s $infolist ./infolists/${infolist.element_identifier} && + + #if $select_settings.setting_file == "template" + python3 '${__tool_directory__}/createSettingsFile.py' + '${__tool_directory__}/mysettings.ini' + '${select_settings.general_param.rtMargin}' + '${select_settings.general_param.rtShift}' + '${select_settings.general_param.use_version}' + '${select_settings.general_param.use_rean_peaks}' + '${select_settings.general_param.add_annotation}' + '${select_settings.shifts.pH}' + '${select_settings.shifts.pM}' + '${select_settings.shifts.pNa}' + '${select_settings.shifts.mH}' + '${select_settings.shifts.mFA}' + '${select_settings.noise_recalibration.electronicNoiseWidth}' + '${select_settings.noise_recalibration.recalibrateBy}' + '${select_settings.noise_recalibration.recalibrateMS1}' + '${select_settings.noise_recalibration.recalibrateMS1Window}' + '${select_settings.noise_recalibration.multiplicityFilter}' + '${select_settings.data_filtering.ppmHighMass}' + '${select_settings.data_filtering.ppmLowMass}' + '${select_settings.data_filtering.massRangeDivision}' + '${select_settings.data_filtering.ppmFine}' + '${select_settings.data_filtering.prelimCut}' + '${select_settings.data_filtering.prelimCutRatio}' + '${select_settings.data_filtering.fineCut}' + '${select_settings.data_filtering.fineCutRatio}' + '${select_settings.data_filtering.specOkLimit}' + '${select_settings.data_filtering.dbeMinLimit}' + '${select_settings.data_filtering.satelliteMzLimit}' + '${select_settings.data_filtering.satelliteIntLimit}' + '${select_settings.raw_settings.ppmFine}' + '${select_settings.raw_settings.mzCoarse}' + '${select_settings.raw_settings.fillPrecursorScan}' + \$(echo `which babel` | sed s/babel//) + '${select_settings.general_param.include_sp_tags}' + '${select_settings.raw_settings.unknownMass}' + && + #else + python3 '${__tool_directory__}/addBabelPath.py' + '${select_settings.setting_file_ext}' + \$(echo `which babel` | sed s/babel//) + && + #end if + + Rscript '${__tool_directory__}/rmassbank.r' + mysettings_galaxy.ini + '${compounds.element_identifier}' + '${mode}' + ./infolists + #for $infile in $param_in: + '${infile.element_identifier}' + #end for + && + + mv mysettings_galaxy.ini $outputINI && + mv results_RA.RData $rafile && + mv results_RF.RData $rffile && + mv Rplots.pdf $pdfplot && + mv results.RData $fllrdata && + zip -r mb_records.zip XX && + mv mb_records.zip $output && + + [ ! -f ./results_Failpeaks.csv ] && touch ./results_Failpeaks.csv && + mv results_Failpeaks.csv $csvfile + ]]> + </command> + <inputs> + <param name="param_in" type="data" format="mzML" multiple="true" label="Input mzML files."/> + <param format="csv" name="compounds" type="data" label="Compound list in CSV format."/> + <param format="csv" name="infolist" type="data" label="Infolist in CSV format."/> + <param name="mode" type="text" label="Mode for RMassBank pipeline."/> + + <conditional name="select_settings"> + <param name="setting_file" type="select" + label="Choose the source if you want to generate settings file or you will supply with your own settings file."> + <option value="template" selected="true">Generate settings file for me</option> + <option value="external">Use external settings file</option> + </param> + <when value="template"> + + <section name="general_param" title="Setting of general parameters."> + <param name="rtMargin" type="float" value="0.4" + label="Deviation (in minutes) allowed the for retention time."/> + <param name="rtShift" type="float" value="0.0" label="Systematic retention time shift."/> + <param name="use_version" type="select" value="2" + label="Which MassBank record version to use; version 2 is advised."> + <option value="2" selected="true">2</option> + <option value="1">1</option> + </param> + <param name="use_rean_peaks" type="select" value="TRUE" label="Include reanalyzed peaks?"> + <option value="TRUE" selected="true">TRUE</option> + <option value="FALSE">FALSE</option> + </param> + <param name="add_annotation" type="select" value="TRUE" + label="Annotate the spectra files with (putative) molecular formulas for fragments?"> + <option value="TRUE" selected="true">TRUE</option> + <option value="FALSE">FALSE</option> + </param> + <param name="include_sp_tags" type="select" value="FALSE" label="Include sp tags?"> + <option value="FALSE" selected="true">FALSE</option> + <option value="TRUE">TRUE</option> + </param> + </section> + + <section name="shifts" title="Shifts of the starting points for RMassBank accession numbers."> + <param name="pH" type="integer" value="0" label="pH ([M+H]+: accession numbers 1-14) "/> + <param name="pM" type="integer" value="16" label="pM ([M]+: 17-30)"/> + <param name="pNa" type="integer" value="32" label="pNa ([M+Na]+: 33-46)"/> + <param name="mH" type="integer" value="50" label="mH ([M-H]-: 51-64)"/> + <param name="mFA" type="integer" value="66" label="mFA ([M+FA]-: 67-80)"/> + </section> + + <section name="noise_recalibration" title="Noise and recalibration settings"> + <param name="electronicNoiseWidth" type="float" value="0.3" + label="Exclusion width of electronic noise peaks (from unmatched peaks, prior to reanalysis)."/> + <param name="recalibrateBy" type="select" value="dppm" label="Recalibration settings:"> + <option value="dppm" selected="true">dppm</option> + <option value="dmz">dmz</option> + </param> + <param name="recalibrateMS1" type="select" value="common" label="Recalibrate MS1:"> + <option value="common" selected="true">with common curve</option> + <option value="separate">separately</option> + <option value="none">none (do not recalibrate)</option> + </param> + <param name="recalibrateMS1Window" type="integer" value="15" + label="Window width to look for MS1 peaks to recalibrate (in ppm integer values):"/> + <param name="multiplicityFilter" type="integer" value="2" + label="Define the multiplicity filtering level, default is 2 (peak occurs at least twice, + set this to 1 if you want to turn this option off, set this to anything > 2 if you want harder filtering"/> + </section> + + <section name="data_filtering" title="Data filtering settings"> + <param name="ppmHighMass" type="integer" value="10" label="ppmHighMass"/> + <param name="ppmLowMass" type="integer" value="15" label="ppmLowMass"/> + <param name="massRangeDivision" type="integer" value="120" label="massRangeDivision"/> + <param name="ppmFine" type="integer" value="5" label="ppmFine"/> + <param name="prelimCut" type="integer" value="1000" label="prelimCut"/> + <param name="prelimCutRatio" type="float" value="0.0" label="prelimCutRatio"/> + <param name="fineCut" type="float" value="0.0" label="fineCut"/> + <param name="fineCutRatio" type="float" value="0.0" label="fineCutRatio"/> + <param name="specOkLimit" type="integer" value="1000" label="specOkLimit"/> + <param name="dbeMinLimit" type="float" value="-0.5" label="dbeMinLimit"/> + <param name="satelliteMzLimit" type="float" value="0.5" label="satelliteMzLimit"/> + <param name="satelliteIntLimit" type="float" value="0.05" label="satelliteIntLimit"/> + </section> + + <section name="raw_settings" title="Degine raw MS retrieval settings"> + <param name="ppmFine" type="integer" value="10" label="ppmFine"/> + <param name="mzCoarse" type="float" value="0.5" label="mzCoarse"/> + <param name="fillPrecursorScan" type="select" value="FALSE" + label="fillPrecursorScan (FALSE for 'good' mzML files which have all the info needed)"> + <option value="TRUE">TRUE</option> + <option value="FALSE" selected="true">FALSE</option> + </param> + <param name="unknownMass" type="select" value="charged" + label="Select how to treat unknown compound masses."> + <option value="charged" selected="true">charged</option> + <option value="neutral">neutral</option> + </param> + </section> + </when> + <when value="external"> + <param name="setting_file_ext" type="data" format="txt" label="Settings file"/> + </when> + </conditional> + + </inputs> + + <outputs> + <data format="txt" name="outputINI" label="mysettings_galaxy.ini"/> + <data format="csv" name="csvfile" label="CSV file with failed peaks."/> + <data format="pdf" name="pdfplot" label="PDF plot."/> + <data format="rdata" name="fllrdata" label="Full R environment."/> + <data format="rdata" name="rafile" label="RData file with re-analyzed spectra (_RA.RData)."/> + <data format="rdata" name="rffile" label="RData file with refiltered spectra (_RF.RData)."/> + <data format="zip" name="output" label="Zipped folder with results."/> + </outputs> + <tests> + <test> + <param name="compounds" value="compoundList.csv"/> + <param name="infolist" value="infolist.csv"/> + <param name="mode" value="pH"/> + <param name="param_in" value="1_3_Trifluoromethylphenyl_piperazin_2819_pos.mzML"/> + <param name="ppmFine" value="5"/> + + <output name="outputINI" value="mysettings_galaxy.ini" ftype="txt" lines_diff="2"/> + <output name="csvfile" value="failedPeaks.csv" ftype="csv" lines_diff="1"/> + <output name="pdfplot" value="plot.pdf" compare="sim_size" delta_frac="0.1"/> + <output name="fllrdata" value="resultsFull.RData" compare="sim_size" delta_frac="0.1"/> + <output name="rafile" value="results_RA.RData" compare="sim_size" delta_frac="0.1"/> + <output name="rffile" value="results_RF.RData" compare="sim_size" delta_frac="0.1"/> + <output name="output" value="output.zip" compare="sim_size" delta_frac="0.1"/> + </test> + </tests> + + <help> + <![CDATA[ + @HELP@ + ]]> + </help> + + <citations> + <citation type="doi">10.1002/jms.3131</citation> + </citations> +</tool>