Mercurial > repos > recetox > recetox_msfinder
view recetox_msfinder.xml @ 5:e7eff0c9baa3 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit c6bc00f50c232c1c7cbb2e6f838c14a0c1c20e05
author | recetox |
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date | Wed, 24 Jan 2024 13:26:32 +0000 |
parents | ae66b58846cd |
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<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy4"> <description>Annotation of fragment peaks in mass spectral libraries.</description> <macros> <import>macros.xml</import> </macros> <expand macro="refs"/> <expand macro="creator" /> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ mkdir output; sh ${write_param}; mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i '$input_data' -m 'MSFINDER.INI' -o 'output/result.msp'; [ -f output/log_smiles.smi ] && sed -i '1s/^/smiles\n/' output/log_smiles.smi; [ -s output/result.msp ] || rm output/result.msp; ]]> </command> <configfiles> <configfile name="write_param"> printf "%s\n" "Ms2Tolerance=$Ms2Tolerance" \ "IsTmsMeoxDerivative=$IsTmsMeoxDerivative" \ "RelativeAbundanceCutOff=$RelativeAbundanceCutOff" \ "Ms1Tolerance=$Ms1Tolerance" \ "MassToleranceType=$MassToleranceType" \ "StructurePredictionTimeOut=$StructurePredictionTimeOut" \ "LewisAndSeniorCheck=$LewisAndSeniorCheck" \ "IsUseRtForFilteringCandidates=False" \ "RtToleranceForStructureElucidation=2.5" \ "IsUsePredictedRtForStructureElucidation=False" \ "Coeff_RtPrediction=-1" \ "Intercept_RtPrediction=-1" \ "IsUseRtInchikeyLibrary=True" \ "IsUsePredictedCcsForStructureElucidation=False" \ "IsUseCcsForFilteringCandidates=True" \ "CcsToleranceForStructureElucidation=10" \ "CanExcuteMS2AdductSearch=False" \ "IsUseXlogpPrediction=False" \ "ElementProbabilityCheck=$ElementProbabilityCheck" \ "IsotopicAbundanceTolerance=$IsotopicAbundanceTolerance" \ "TreeDepth=$TreeDepth" \ "$element_ratio_check" \ "IsUseEiFragmentDB=$IsUseEiFragmentDB" >MSFINDER.INI #set element_selected = "\n".join([str($element) for $element in str($element_selection_option).split(",")]) printf "%s\n" "$element_selected" >> MSFINDER.INI </configfile> </configfiles> <inputs> <expand macro="input" /> <expand macro="parameter" /> <param name="element_selection_option" type="select" label="Element selection" multiple="true" optional="true" help="Generate formula candidates that just contain the elements selected by the users. Check 'IsTmsMeoxDerivative' if you want to annotate EI-MS spectra."> <expand macro="element_select" /> </param> </inputs> <outputs> <expand macro="output" /> </outputs> <tests> <test> <param name="input_data" value="test.msp" ftype="msp" /> <output_collection name="output" type="list"> <element name="result" file="out.msp" lines_diff="16"/> </output_collection> <!-- This is set to 16 since msfinder sometimes places double bonds between certain atoms and sometimes not - there are 16 such cases in this file. --> </test> <test> <param name="input_data" value="test.msp" ftype="msp" /> <param name="element_ratio_check" value="ExtendedRange=TRUE"/> <param name="TreeDepth" value="3"/> <param name="element_selection_option" value="Ocheck=True,Ncheck=True,Pcheck=True,Scheck=True,Fcheck=True,ClCheck=True,BrCheck=True,Icheck=True,SiCheck=True"/> <output_collection name="output" type="list"> <element name="result" file="test2_out.msp" lines_diff="24"/> </output_collection> </test> <test> <param name="input_data" value="test_log.msp" ftype="msp" /> <output_collection name="output" type="list"> <element name="log_smiles" file="log_smiles.smi" /> </output_collection> </test> </tests> <help> <![CDATA[ @HELP@ ]]> </help> <citations> <expand macro="citations" /> </citations> </tool>