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view ramclustr_define_experiment.xml @ 4:5f2b58dadb39 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit f79a5b51599254817727bc9028b9797ea994cb4e
author | recetox |
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date | Tue, 27 Jun 2023 14:29:49 +0000 |
parents | 049285068dad |
children | 7bbdcce50541 |
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<tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2+galaxy0" profile="21.09"> <description>Definition of experimental design used for record keeping and writing spectra data.</description> <macros> <import>macros.xml</import> </macros> <edam_operations> <edam_operation>operation_3429</edam_operation> </edam_operations> <expand macro='annotation'/> <expand macro="creator"/> <command detect_errors="exit_code"><![CDATA[ sh ${ramclustr_define_experiment_cli} ]]> </command> <configfiles> <configfile name="ramclustr_define_experiment_cli"> python3 ${__tool_directory__}/ramclustr_define_experiment_wrapper.py \ --Experiment "$design.Experiment" \ --Species "$design.Species" \ --Sample "$design.Sample" \ --Contributer "$design.Contributor" \ --platform "$platform.platform_choice.choice" \ #if $platform.platform_choice.choice == "GC-MS": --chrominst "$platform.platform_choice.chrominst" \ --msinst "$platform.platform_choice.msinst" \ --column "$platform.platform_choice.column" \ --InletTemp "$platform.platform_choice.InletTemp" \ --TransferTemp "$platform.platform_choice.TransferTemp" \ --mstype "$platform.platform_choice.gc_mstype" \ --msmode "$platform.platform_choice.msmode" \ --ionization "$platform.platform_choice.gc_ionization" \ --msscanrange "$platform.platform_choice.msscanrange" \ --scantime "$platform.platform_choice.scantime" \ --deriv "$platform.platform_choice.deriv" \ --MSlevs "$platform.platform_choice.MSlevs" \ #else: --chrominst "$platform.platform_choice.chrominst" \ --msinst "$platform.platform_choice.msinst" \ --column "$platform.platform_choice.column" \ --solvA "$platform.platform_choice.solvA" \ --solvB "$platform.platform_choice.solvB" \ --CE1 "$platform.platform_choice.CE1" \ --CE2 "$platform.platform_choice.CE2" \ --mstype "$platform.platform_choice.lc_mstype" \ --msmode "$platform.platform_choice.msmode" \ --ionization "$platform.platform_choice.lc_ionization" \ --colgas "$platform.platform_choice.colgas" \ --msscanrange "$platform.platform_choice.msscanrange" \ --conevol "$platform.platform_choice.conevol" \ --MSlevs "$platform.platform_choice.MSlevs" \ #end if --output_file "$RAMClustR_experiment" </configfile> </configfiles> <inputs> <section name="design" title="Experimental Design" expanded="true"> <param name="Experiment" type="text" label="Experiment name (no spaces)."> <validator type="empty_field"/> </param> <param name="Species" type="text" label="Genus species from which samples are derived."/> <param name="Sample" type="text" label="Type of sample (e.g., serum, leaf)."/> <param name="Contributor" type="text" label="Your or your PI's name."/> </section> <section name="platform" title="Platform" expanded="true"> <conditional name="platform_choice"> <param name="choice" type="select" label="Choose platform:"> <option value="GC-MS" selected="true">GC-MS</option> <option value="LC-MS">LC-MS</option> </param> <when value="GC-MS"> <param name="chrominst" type="text" label="Model of GC instrument."/> <param name="msinst" type="text" label="Model of MS instrument."/> <param name="column" type="text" label="Column description."/> <param name="InletTemp" type="text" label="Temperature of inlet."/> <param name="TransferTemp" type="text" label="Temperature of GC to MS transfer line."/> <param name="gc_mstype" type="select" label="Type of mass spectrometer:"> <option value="QQQ" selected="true">QQQ</option> <option value="TOF">TOF</option> <option value="QTOF">QTOF</option> <option value="Orbi">Orbi</option> <option value="Q">Q</option> </param> <param name="msmode" type="select" label="Ion mode:"> <option value="positive" selected="true">positive</option> <option value="negative">negative</option> </param> <param name="gc_ionization" type="select" label="Ionization:"> <option value="EI" selected="true">EI</option> <option value="AP">AP</option> <option value="CI">CI</option> </param> <param name="msscanrange" type="text" label="Scan range used for acquisition."/> <param name="scantime" type="float" value="0.2" label="Time for each full scan spectrum (e.g. 0.2 seconds)."/> <param name="deriv" type="select" label="Derivitization:"> <option value="TMS" selected="true">TMS</option> <option value="TBDMS">TBDMS</option> <option value="None">None</option> </param> <param name="MSlevs" type="float" value="1" label="Number of levels of energy acquired - 1 typically."/> </when> <when value="LC-MS"> <param name="chrominst" type="text" label="Model of LC instrument."/> <param name="msinst" type="text" label="Model of MS instrument."/> <param name="column" type="text" label="Column description."/> <param name="solvA" type="text" label="Solvent A composition."/> <param name="solvB" type="text" label="Solvent B composition."/> <param name="CE1" type="text" label="Collision energy of acquisition of MS data."/> <param name="CE2" type="text" label="Collision energy of acquisition for MSe/idMSMS data (when applicable)."/> <param name="lc_mstype" type="select" label="Type of mass spectrometer:"> <option value="QQQ" selected="true">QQQ</option> <option value="TOF">TOF</option> <option value="QTOF">QTOF</option> <option value="Orbi">Orbi</option> <option value="Q">Q</option> </param> <param name="msmode" type="select" label="Ion mode:"> <option value="positive" selected="true">positive</option> <option value="negative">negative</option> </param> <param name="lc_ionization" type="select" label="Ionization:"> <option value="ESI" selected="true">ESI</option> <option value="APCI">APCI</option> </param> <param name="colgas" type="text" label="Gas used for collisional dissociation."/> <param name="msscanrange" type="text" label="Scan range used for acquisition."/> <param name="conevol" type="text" label="Cone voltage used for acquisition."/> <param name="MSlevs" type="float" value="1" label="number of levels of energy in XCMS object data - 1 typically."/> </when> </conditional> </section> </inputs> <outputs> <data label="RAMClustR experiment definition" name="RAMClustR_experiment" format="csv" /> </outputs> <tests> <test><!-- TEST 1 --> <section name="design"> <param name="Experiment" value="experiment_gc"/> <param name="Species" value="mus musculus"/> <param name="Sample" value="serum"/> <param name="Contributor" value="recetox"/> </section> <section name="platform"> <section name="platform_choice"> <param name="choice" value="GC-MS"/> <param name="chrominst" value="ISQ 7000"/> <param name="msinst" value="ISQ7K-VPI"/> <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/> <param name="InletTemp" value="33"/> <param name="TransferTemp" value="23"/> <param name="gc_mstype" value="QTOF"/> <param name="msmode" value="positive"/> <param name="gc_ionization" value="AP"/> <param name="msscanrange" value="100"/> <param name="scantime" value="0.2"/> <param name="deriv" value="TMS"/> <param name="MSlevs" value="1.0"/> </section> </section> <output name="RAMClustR_experiment" file="gc-ramclustr-define-experiment.csv" ftype="csv"/> </test> <test><!-- TEST 2 --> <section name="design"> <param name="Experiment" value="experiment_lc"/> <param name="Species" value="mus musculus"/> <param name="Sample" value="serum"/> <param name="Contributor" value="recetox"/> </section> <section name="platform"> <section name="platform_choice"> <param name="choice" value="LC-MS"/> <param name="chrominst" value="UltiMateX 3000 BioRS System"/> <param name="msinst" value="FSN04-10000"/> <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/> <param name="solvA" value="H20"/> <param name="solvB" value="CO2"/> <param name="CE1" value="50"/> <param name="CE2" value="100"/> <param name="lc_mstype" value="Q"/> <param name="msmode" value="negative"/> <param name="lc_ionization" value="ESI"/> <param name="colgas" value="He"/> <param name="msscanrange" value="1000"/> <param name="conevol" value="12"/> <param name="MSlevs" value="1.0"/> </section> </section> <output name="RAMClustR_experiment" file="lc-ramclustr-define-experiment.csv" ftype="csv"/> </test> </tests> <help> <![CDATA[ @HELP_experiment@ ]]> </help> <expand macro="citations" /> </tool>