Mercurial > repos > recetox > recetox_msfinder
view recetox_msfinder.xml @ 4:ae66b58846cd draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit ad60bf881a8fd00546909c76d65ea3c6b65a4fe9
author | recetox |
---|---|
date | Fri, 01 Dec 2023 09:23:21 +0000 |
parents | d1f44632f206 |
children | e7eff0c9baa3 |
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<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy3"> <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> <![CDATA[ mkdir output; sh ${write_param}; mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o 'output/result.msp'; [ -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" >MSFINDER.INI </configfile> </configfiles> <inputs> <expand macro="input" /> <expand macro="parameter" /> <!-- <section name="element_selection" title="Element Selection" expanded="true" help="Generate formula candidates that just contain the elements selected by the users."> <expand macro="element_check_parameter" /> </section> --> </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_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>