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Merge pull request #217 from xtrojak/ramclustr-define-experiment
RAMClustR experimental design input
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| @@ -0,0 +1,198 @@ | ||
| <tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.0"> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <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> |
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