From f34c79c65c8d59f59828f5faf0f6a8861afbef58 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 12 Apr 2024 13:32:47 +0200 Subject: [PATCH] copy instead of symlink https://github.com/OpenMS/OpenMS/issues/7439 --- tools/openms/AccurateMassSearch.xml | 14 +++++++------- tools/openms/AssayGeneratorMetabo.xml | 8 ++++---- tools/openms/BaselineFilter.xml | 2 +- tools/openms/CVInspector.xml | 6 +++--- tools/openms/ClusterMassTraces.xml | 2 +- tools/openms/ClusterMassTracesByPrecursor.xml | 4 ++-- tools/openms/CometAdapter.xml | 6 +++--- tools/openms/ConsensusID.xml | 4 ++-- tools/openms/ConsensusMapNormalizer.xml | 2 +- tools/openms/DTAExtractor.xml | 2 +- tools/openms/DatabaseFilter.xml | 4 ++-- tools/openms/DatabaseSuitability.xml | 10 +++++----- tools/openms/DeMeanderize.xml | 2 +- tools/openms/Decharger.xml | 2 +- tools/openms/DecoyDatabase.xml | 4 ++-- tools/openms/Digestor.xml | 2 +- tools/openms/DigestorMotif.xml | 2 +- tools/openms/EICExtractor.xml | 10 +++++----- tools/openms/ERPairFinder.xml | 4 ++-- tools/openms/Epifany.xml | 6 +++--- tools/openms/ExternalCalibration.xml | 2 +- tools/openms/FLASHDeconv.xml | 2 +- tools/openms/FalseDiscoveryRate.xml | 2 +- tools/openms/FeatureFinderCentroided.xml | 4 ++-- tools/openms/FeatureFinderIdentification.xml | 8 ++++---- tools/openms/FeatureFinderIsotopeWavelet.xml | 2 +- tools/openms/FeatureFinderMRM.xml | 2 +- tools/openms/FeatureFinderMetabo.xml | 2 +- tools/openms/FeatureFinderMetaboIdent.xml | 4 ++-- tools/openms/FeatureFinderMultiplex.xml | 2 +- tools/openms/FeatureLinkerLabeled.xml | 2 +- tools/openms/FeatureLinkerUnlabeled.xml | 6 +++--- tools/openms/FeatureLinkerUnlabeledKD.xml | 6 +++--- tools/openms/FeatureLinkerUnlabeledQT.xml | 6 +++--- tools/openms/FileConverter.xml | 2 +- tools/openms/FileFilter.xml | 8 ++++---- tools/openms/FileInfo.xml | 2 +- tools/openms/FileMerger.xml | 4 ++-- tools/openms/FuzzyDiff.xml | 4 ++-- tools/openms/GNPSExport.xml | 6 +++--- tools/openms/HighResPrecursorMassCorrector.xml | 4 ++-- tools/openms/IDConflictResolver.xml | 2 +- tools/openms/IDExtractor.xml | 2 +- tools/openms/IDFileConverter.xml | 4 ++-- tools/openms/IDFilter.xml | 12 ++++++------ tools/openms/IDMapper.xml | 6 +++--- tools/openms/IDMassAccuracy.xml | 8 ++++---- tools/openms/IDMerger.xml | 6 +++--- tools/openms/IDPosteriorErrorProbability.xml | 2 +- tools/openms/IDRTCalibration.xml | 2 +- tools/openms/IDRipper.xml | 2 +- tools/openms/IDScoreSwitcher.xml | 2 +- tools/openms/IDSplitter.xml | 2 +- tools/openms/InternalCalibration.xml | 6 +++--- tools/openms/IsobaricAnalyzer.xml | 2 +- tools/openms/JSONExporter.xml | 2 +- tools/openms/LuciphorAdapter.xml | 4 ++-- tools/openms/MRMMapper.xml | 4 ++-- tools/openms/MRMPairFinder.xml | 4 ++-- tools/openms/MRMTransitionGroupPicker.xml | 4 ++-- tools/openms/MSFraggerAdapter.xml | 4 ++-- tools/openms/MSGFPlusAdapter.xml | 6 +++--- tools/openms/MSstatsConverter.xml | 8 ++++---- tools/openms/MaRaClusterAdapter.xml | 8 ++++---- tools/openms/MapAlignerIdentification.xml | 8 ++++---- tools/openms/MapAlignerPoseClustering.xml | 6 +++--- tools/openms/MapAlignerSpectrum.xml | 4 ++-- tools/openms/MapAlignerTreeGuided.xml | 4 ++-- tools/openms/MapNormalizer.xml | 2 +- tools/openms/MapRTTransformer.xml | 4 ++-- tools/openms/MapStatistics.xml | 2 +- tools/openms/MascotAdapter.xml | 2 +- tools/openms/MascotAdapterOnline.xml | 2 +- tools/openms/MassCalculator.xml | 2 +- tools/openms/MassTraceExtractor.xml | 2 +- tools/openms/MetaProSIP.xml | 6 +++--- tools/openms/MetaboliteAdductDecharger.xml | 2 +- tools/openms/MetaboliteSpectralMatcher.xml | 4 ++-- tools/openms/MultiplexResolver.xml | 4 ++-- tools/openms/MzMLSplitter.xml | 2 +- tools/openms/MzTabExporter.xml | 2 +- tools/openms/NoiseFilterGaussian.xml | 2 +- tools/openms/NoiseFilterSGolay.xml | 2 +- tools/openms/NovorAdapter.xml | 4 ++-- tools/openms/NucleicAcidSearchEngine.xml | 6 +++--- tools/openms/OpenMSInfo.xml | 2 +- tools/openms/OpenPepXL.xml | 8 ++++---- tools/openms/OpenPepXLLF.xml | 6 +++--- tools/openms/OpenSwathAnalyzer.xml | 10 +++++----- tools/openms/OpenSwathAssayGenerator.xml | 6 +++--- .../openms/OpenSwathChromatogramExtractor.xml | 8 ++++---- tools/openms/OpenSwathConfidenceScoring.xml | 6 +++--- tools/openms/OpenSwathDIAPreScoring.xml | 6 +++--- tools/openms/OpenSwathDecoyGenerator.xml | 2 +- tools/openms/OpenSwathFeatureXMLToTSV.xml | 6 +++--- tools/openms/OpenSwathFileSplitter.xml | 2 +- tools/openms/OpenSwathMzMLFileCacher.xml | 2 +- tools/openms/OpenSwathRTNormalizer.xml | 8 ++++---- tools/openms/OpenSwathRewriteToFeatureXML.xml | 4 ++-- tools/openms/OpenSwathWorkflow.xml | 12 ++++++------ tools/openms/PSMFeatureExtractor.xml | 4 ++-- tools/openms/PeakPickerHiRes.xml | 2 +- tools/openms/PeakPickerIterative.xml | 2 +- tools/openms/PeakPickerWavelet.xml | 2 +- tools/openms/PeptideIndexer.xml | 4 ++-- tools/openms/PercolatorAdapter.xml | 14 +++++++------- tools/openms/PhosphoScoring.xml | 4 ++-- tools/openms/PrecursorMassCorrector.xml | 4 ++-- tools/openms/ProteinInference.xml | 4 ++-- tools/openms/ProteinQuantifier.xml | 6 +++--- tools/openms/ProteinResolver.xml | 8 ++++---- tools/openms/QCCalculator.xml | 8 ++++---- tools/openms/QCEmbedder.xml | 8 ++++---- tools/openms/QCExporter.xml | 4 ++-- tools/openms/QCExtractor.xml | 4 ++-- tools/openms/QCImporter.xml | 6 +++--- tools/openms/QCMerger.xml | 4 ++-- tools/openms/QCShrinker.xml | 4 ++-- tools/openms/QualityControl.xml | 18 +++++++++--------- tools/openms/RNADigestor.xml | 2 +- tools/openms/RNAMassCalculator.xml | 2 +- tools/openms/RNPxlSearch.xml | 4 ++-- tools/openms/RNPxlXICFilter.xml | 4 ++-- tools/openms/SageAdapter.xml | 6 +++--- tools/openms/SeedListGenerator.xml | 2 +- tools/openms/SemanticValidator.xml | 8 ++++---- tools/openms/SequenceCoverageCalculator.xml | 4 ++-- tools/openms/SimpleSearchEngine.xml | 4 ++-- tools/openms/SiriusAdapter.xml | 4 ++-- tools/openms/SpecLibCreator.xml | 4 ++-- tools/openms/SpecLibSearcher.xml | 6 +++--- tools/openms/SpectraFilterBernNorm.xml | 2 +- tools/openms/SpectraFilterMarkerMower.xml | 2 +- tools/openms/SpectraFilterNLargest.xml | 2 +- tools/openms/SpectraFilterNormalizer.xml | 2 +- tools/openms/SpectraFilterParentPeakMower.xml | 2 +- tools/openms/SpectraFilterScaler.xml | 2 +- tools/openms/SpectraFilterSqrtMower.xml | 2 +- tools/openms/SpectraFilterThresholdMower.xml | 2 +- tools/openms/SpectraFilterWindowMower.xml | 2 +- tools/openms/SpectraMerger.xml | 2 +- tools/openms/SpectraSTSearchAdapter.xml | 12 ++++++------ tools/openms/StaticModification.xml | 2 +- tools/openms/TICCalculator.xml | 2 +- tools/openms/TOFCalibration.xml | 8 ++++---- tools/openms/TargetedFileConverter.xml | 2 +- tools/openms/TextExporter.xml | 2 +- tools/openms/TriqlerConverter.xml | 8 ++++---- tools/openms/XFDR.xml | 2 +- tools/openms/XMLValidator.xml | 4 ++-- tools/openms/XTandemAdapter.xml | 6 +++--- 151 files changed, 333 insertions(+), 333 deletions(-) diff --git a/tools/openms/AccurateMassSearch.xml b/tools/openms/AccurateMassSearch.xml index ea9cd8202..293a31b3e 100644 --- a/tools/openms/AccurateMassSearch.xml +++ b/tools/openms/AccurateMassSearch.xml @@ -14,35 +14,35 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_annotation && #end if #if $positive_adducts: mkdir positive_adducts && - ln -s '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' && + cp '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' && #end if #if $negative_adducts: mkdir negative_adducts && - ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' && + cp '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' && #end if #if $db.mapping_cond.mapping: mkdir db.mapping_cond.mapping && #if $db.mapping_cond.mapping_select == "no" mkdir ${' '.join(["'db.mapping_cond.mapping/%s'" % (i) for i, f in enumerate($db.mapping_cond.mapping) if f])} && - ${' '.join(["ln -s '%s' 'db.mapping_cond.mapping/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])} + ${' '.join(["cp '%s' 'db.mapping_cond.mapping/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])} #else - ln -s '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' && + cp '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' && #end if #end if #if $db.struct_cond.struct: mkdir db.struct_cond.struct && #if $db.struct_cond.struct_select == "no" mkdir ${' '.join(["'db.struct_cond.struct/%s'" % (i) for i, f in enumerate($db.struct_cond.struct) if f])} && - ${' '.join(["ln -s '%s' 'db.struct_cond.struct/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])} + ${' '.join(["cp '%s' 'db.struct_cond.struct/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])} #else - ln -s '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' && + cp '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' && #end if #end if diff --git a/tools/openms/AssayGeneratorMetabo.xml b/tools/openms/AssayGeneratorMetabo.xml index f6abded3d..cb90096b7 100644 --- a/tools/openms/AssayGeneratorMetabo.xml +++ b/tools/openms/AssayGeneratorMetabo.xml @@ -16,16 +16,16 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir in_id_cond.in_id && #if $in_id_cond.in_id_select == "no" mkdir ${' '.join(["'in_id_cond.in_id/%s'" % (i) for i, f in enumerate($in_id_cond.in_id) if f])} && -${' '.join(["ln -s '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])} +${' '.join(["cp '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])} #else -ln -s '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' && +cp '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' && #end if mkdir out && diff --git a/tools/openms/BaselineFilter.xml b/tools/openms/BaselineFilter.xml index e7f526836..67062e980 100644 --- a/tools/openms/BaselineFilter.xml +++ b/tools/openms/BaselineFilter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/CVInspector.xml b/tools/openms/CVInspector.xml index 19d14f420..af8c3210d 100644 --- a/tools/openms/CVInspector.xml +++ b/tools/openms/CVInspector.xml @@ -16,12 +16,12 @@ mkdir cv_files_cond.cv_files && #if $cv_files_cond.cv_files_select == "no" mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} && -${' '.join(["ln -s '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])} +${' '.join(["cp '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])} #else -ln -s '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' && +cp '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' && #end if mkdir mapping_file && -ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && +cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir html && #end if diff --git a/tools/openms/ClusterMassTraces.xml b/tools/openms/ClusterMassTraces.xml index 73bdea980..1b3fda50d 100644 --- a/tools/openms/ClusterMassTraces.xml +++ b/tools/openms/ClusterMassTraces.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/ClusterMassTracesByPrecursor.xml b/tools/openms/ClusterMassTracesByPrecursor.xml index c5b7c15ae..f1a0139a7 100644 --- a/tools/openms/ClusterMassTracesByPrecursor.xml +++ b/tools/openms/ClusterMassTracesByPrecursor.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in_ms1 && -ln -s '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' && +cp '$in_ms1' 'in_ms1/${re.sub("[^\w\-_]", "_", $in_ms1.element_identifier)}.$gxy2omsext($in_ms1.ext)' && mkdir in_swath && -ln -s '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' && +cp '$in_swath' 'in_swath/${re.sub("[^\w\-_]", "_", $in_swath.element_identifier)}.$gxy2omsext($in_swath.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/CometAdapter.xml b/tools/openms/CometAdapter.xml index 7bb8f9d46..cc5beef35 100644 --- a/tools/openms/CometAdapter.xml +++ b/tools/openms/CometAdapter.xml @@ -14,16 +14,16 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir pin_out && #end if #if $default_params_file: mkdir default_params_file && - ln -s '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' && + cp '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' && #end if ## Main program call diff --git a/tools/openms/ConsensusID.xml b/tools/openms/ConsensusID.xml index 7e9b9faf2..d6bd67555 100644 --- a/tools/openms/ConsensusID.xml +++ b/tools/openms/ConsensusID.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && diff --git a/tools/openms/ConsensusMapNormalizer.xml b/tools/openms/ConsensusMapNormalizer.xml index 464f9de9b..447ac7167 100644 --- a/tools/openms/ConsensusMapNormalizer.xml +++ b/tools/openms/ConsensusMapNormalizer.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/DTAExtractor.xml b/tools/openms/DTAExtractor.xml index e6a501749..4f2d99237 100644 --- a/tools/openms/DTAExtractor.xml +++ b/tools/openms/DTAExtractor.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && ## Main program call diff --git a/tools/openms/DatabaseFilter.xml b/tools/openms/DatabaseFilter.xml index 8636e4912..943cb795f 100644 --- a/tools/openms/DatabaseFilter.xml +++ b/tools/openms/DatabaseFilter.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/DatabaseSuitability.xml b/tools/openms/DatabaseSuitability.xml index 6e63340e0..4c0397beb 100644 --- a/tools/openms/DatabaseSuitability.xml +++ b/tools/openms/DatabaseSuitability.xml @@ -14,15 +14,15 @@ ## Preprocessing mkdir in_id && -ln -s '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' && +cp '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' && mkdir in_spec && -ln -s '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' && +cp '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' && mkdir in_novo && -ln -s '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' && +cp '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && mkdir novo_database && -ln -s '$novo_database' 'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)' && +cp '$novo_database' 'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if diff --git a/tools/openms/DeMeanderize.xml b/tools/openms/DeMeanderize.xml index 254cd5e78..d5b35b0f4 100644 --- a/tools/openms/DeMeanderize.xml +++ b/tools/openms/DeMeanderize.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/Decharger.xml b/tools/openms/Decharger.xml index 0f4d51d4d..5b9b83910 100644 --- a/tools/openms/Decharger.xml +++ b/tools/openms/Decharger.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out_cm && #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_fm && diff --git a/tools/openms/DecoyDatabase.xml b/tools/openms/DecoyDatabase.xml index c4cebb3f6..70b2e6f60 100644 --- a/tools/openms/DecoyDatabase.xml +++ b/tools/openms/DecoyDatabase.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && diff --git a/tools/openms/Digestor.xml b/tools/openms/Digestor.xml index c33db9f4c..ba58260c4 100644 --- a/tools/openms/Digestor.xml +++ b/tools/openms/Digestor.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/DigestorMotif.xml b/tools/openms/DigestorMotif.xml index 3396dbf6f..4571b2afd 100644 --- a/tools/openms/DigestorMotif.xml +++ b/tools/openms/DigestorMotif.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/EICExtractor.xml b/tools/openms/EICExtractor.xml index 136888a68..a69222e20 100644 --- a/tools/openms/EICExtractor.xml +++ b/tools/openms/EICExtractor.xml @@ -16,21 +16,21 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #if $in_header_cond.in_header: mkdir in_header_cond.in_header && #if $in_header_cond.in_header_select == "no" mkdir ${' '.join(["'in_header_cond.in_header/%s'" % (i) for i, f in enumerate($in_header_cond.in_header) if f])} && - ${' '.join(["ln -s '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])} + ${' '.join(["cp '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])} #else - ln -s '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' && + cp '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' && #end if #end if mkdir pos && -ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && +cp '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && mkdir out && #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir auto_rt_out_debug_TIC && diff --git a/tools/openms/ERPairFinder.xml b/tools/openms/ERPairFinder.xml index 506348198..fea6b0729 100644 --- a/tools/openms/ERPairFinder.xml +++ b/tools/openms/ERPairFinder.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir pair_in && -ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' && +cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' && mkdir out && #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir feature_out && diff --git a/tools/openms/Epifany.xml b/tools/openms/Epifany.xml index a8a509251..3b68b80c0 100644 --- a/tools/openms/Epifany.xml +++ b/tools/openms/Epifany.xml @@ -16,13 +16,13 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #if $exp_design: mkdir exp_design && - ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' && + cp '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' && #end if mkdir out && diff --git a/tools/openms/ExternalCalibration.xml b/tools/openms/ExternalCalibration.xml index dfcfc2d65..69d79c719 100644 --- a/tools/openms/ExternalCalibration.xml +++ b/tools/openms/ExternalCalibration.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/FLASHDeconv.xml b/tools/openms/FLASHDeconv.xml index ad8d4588d..e903f79f8 100644 --- a/tools/openms/FLASHDeconv.xml +++ b/tools/openms/FLASHDeconv.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_spec_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_spec && diff --git a/tools/openms/FalseDiscoveryRate.xml b/tools/openms/FalseDiscoveryRate.xml index cb8705c34..011c89433 100644 --- a/tools/openms/FalseDiscoveryRate.xml +++ b/tools/openms/FalseDiscoveryRate.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/FeatureFinderCentroided.xml b/tools/openms/FeatureFinderCentroided.xml index 8be01d099..9b5fd2b19 100644 --- a/tools/openms/FeatureFinderCentroided.xml +++ b/tools/openms/FeatureFinderCentroided.xml @@ -14,11 +14,11 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $seeds: mkdir seeds && - ln -s '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' && + cp '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' && #end if #if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_mzq && diff --git a/tools/openms/FeatureFinderIdentification.xml b/tools/openms/FeatureFinderIdentification.xml index c2b8d445a..595267e9c 100644 --- a/tools/openms/FeatureFinderIdentification.xml +++ b/tools/openms/FeatureFinderIdentification.xml @@ -14,12 +14,12 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && #if $id_ext: mkdir id_ext && - ln -s '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' && + cp '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' && #end if mkdir out && #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') @@ -37,7 +37,7 @@ mkdir out && ## advanced options #if $adv_opts.candidates_in: mkdir adv_opts.candidates_in && - ln -s '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' && + cp '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' && #end if diff --git a/tools/openms/FeatureFinderIsotopeWavelet.xml b/tools/openms/FeatureFinderIsotopeWavelet.xml index e2d56b285..d79c661b5 100644 --- a/tools/openms/FeatureFinderIsotopeWavelet.xml +++ b/tools/openms/FeatureFinderIsotopeWavelet.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/FeatureFinderMRM.xml b/tools/openms/FeatureFinderMRM.xml index 3db5bc3ea..e72e102eb 100644 --- a/tools/openms/FeatureFinderMRM.xml +++ b/tools/openms/FeatureFinderMRM.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/FeatureFinderMetabo.xml b/tools/openms/FeatureFinderMetabo.xml index 39982c509..229859888 100644 --- a/tools/openms/FeatureFinderMetabo.xml +++ b/tools/openms/FeatureFinderMetabo.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_chrom && diff --git a/tools/openms/FeatureFinderMetaboIdent.xml b/tools/openms/FeatureFinderMetaboIdent.xml index 45797ec3d..ac3e00653 100644 --- a/tools/openms/FeatureFinderMetaboIdent.xml +++ b/tools/openms/FeatureFinderMetaboIdent.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && mkdir out && #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir lib_out && diff --git a/tools/openms/FeatureFinderMultiplex.xml b/tools/openms/FeatureFinderMultiplex.xml index dd29a3f9d..3c99ea56d 100644 --- a/tools/openms/FeatureFinderMultiplex.xml +++ b/tools/openms/FeatureFinderMultiplex.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if diff --git a/tools/openms/FeatureLinkerLabeled.xml b/tools/openms/FeatureLinkerLabeled.xml index 11632834a..a80e492d5 100644 --- a/tools/openms/FeatureLinkerLabeled.xml +++ b/tools/openms/FeatureLinkerLabeled.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/FeatureLinkerUnlabeled.xml b/tools/openms/FeatureLinkerUnlabeled.xml index c194cf45b..50e56465f 100644 --- a/tools/openms/FeatureLinkerUnlabeled.xml +++ b/tools/openms/FeatureLinkerUnlabeled.xml @@ -16,14 +16,14 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && #if $design: mkdir design && - ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && + cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if ## Main program call diff --git a/tools/openms/FeatureLinkerUnlabeledKD.xml b/tools/openms/FeatureLinkerUnlabeledKD.xml index f6311a5fb..9b83f5483 100644 --- a/tools/openms/FeatureLinkerUnlabeledKD.xml +++ b/tools/openms/FeatureLinkerUnlabeledKD.xml @@ -16,14 +16,14 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && #if $design: mkdir design && - ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && + cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if ## Main program call diff --git a/tools/openms/FeatureLinkerUnlabeledQT.xml b/tools/openms/FeatureLinkerUnlabeledQT.xml index 61771fc45..e754b7dfa 100644 --- a/tools/openms/FeatureLinkerUnlabeledQT.xml +++ b/tools/openms/FeatureLinkerUnlabeledQT.xml @@ -16,14 +16,14 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && #if $design: mkdir design && - ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && + cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if ## Main program call diff --git a/tools/openms/FileConverter.xml b/tools/openms/FileConverter.xml index 8042c190d..d9acfd0cc 100644 --- a/tools/openms/FileConverter.xml +++ b/tools/openms/FileConverter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/FileFilter.xml b/tools/openms/FileFilter.xml index 1b939769a..e8b036822 100644 --- a/tools/openms/FileFilter.xml +++ b/tools/openms/FileFilter.xml @@ -14,19 +14,19 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $spectra.blackorwhitelist.file: mkdir spectra.blackorwhitelist.file && - ln -s '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' && + cp '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' && #end if #if $consensus.blackorwhitelist.file: mkdir consensus.blackorwhitelist.file && - ln -s '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' && + cp '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' && #end if #if $id.blacklist: mkdir id.blacklist && - ln -s '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' && + cp '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' && #end if ## Main program call diff --git a/tools/openms/FileInfo.xml b/tools/openms/FileInfo.xml index afc28081f..a8eb96a4d 100644 --- a/tools/openms/FileInfo.xml +++ b/tools/openms/FileInfo.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_tsv && diff --git a/tools/openms/FileMerger.xml b/tools/openms/FileMerger.xml index 5b5b7ad50..05fa073a6 100644 --- a/tools/openms/FileMerger.xml +++ b/tools/openms/FileMerger.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') diff --git a/tools/openms/FuzzyDiff.xml b/tools/openms/FuzzyDiff.xml index d6e1737fd..d686b4535 100644 --- a/tools/openms/FuzzyDiff.xml +++ b/tools/openms/FuzzyDiff.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in1 && -ln -s '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' && +cp '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' && mkdir in2 && -ln -s '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' && +cp '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' && ## Main program call diff --git a/tools/openms/GNPSExport.xml b/tools/openms/GNPSExport.xml index 4c6705c4b..405e899fa 100644 --- a/tools/openms/GNPSExport.xml +++ b/tools/openms/GNPSExport.xml @@ -14,13 +14,13 @@ ## Preprocessing mkdir in_cm && -ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' && +cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' && mkdir in_mzml_cond.in_mzml && #if $in_mzml_cond.in_mzml_select == "no" mkdir ${' '.join(["'in_mzml_cond.in_mzml/%s'" % (i) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} && -${' '.join(["ln -s '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} +${' '.join(["cp '%s' 'in_mzml_cond.in_mzml/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_mzml_cond.in_mzml) if f])} #else -ln -s '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' && +cp '$in_mzml_cond.in_mzml' 'in_mzml_cond.in_mzml/${re.sub("[^\w\-_]", "_", $in_mzml_cond.in_mzml.element_identifier)}.$gxy2omsext($in_mzml_cond.in_mzml.ext)' && #end if mkdir out && mkdir out_quantification && diff --git a/tools/openms/HighResPrecursorMassCorrector.xml b/tools/openms/HighResPrecursorMassCorrector.xml index 774cc3b80..e9bd597c5 100644 --- a/tools/openms/HighResPrecursorMassCorrector.xml +++ b/tools/openms/HighResPrecursorMassCorrector.xml @@ -14,14 +14,14 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_csv && #end if #if $feature.in: mkdir feature.in && - ln -s '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' && + cp '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' && #end if ## Main program call diff --git a/tools/openms/IDConflictResolver.xml b/tools/openms/IDConflictResolver.xml index 090c733af..50bc2b16e 100644 --- a/tools/openms/IDConflictResolver.xml +++ b/tools/openms/IDConflictResolver.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/IDExtractor.xml b/tools/openms/IDExtractor.xml index 504d54cc7..4e766bb1b 100644 --- a/tools/openms/IDExtractor.xml +++ b/tools/openms/IDExtractor.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/IDFileConverter.xml b/tools/openms/IDFileConverter.xml index 8ec0e1a91..1506e295a 100644 --- a/tools/openms/IDFileConverter.xml +++ b/tools/openms/IDFileConverter.xml @@ -14,11 +14,11 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $mz_file: mkdir mz_file && - ln -s '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' && + cp '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' && #end if ## Main program call diff --git a/tools/openms/IDFilter.xml b/tools/openms/IDFilter.xml index 6ca4b65e9..69acc8021 100644 --- a/tools/openms/IDFilter.xml +++ b/tools/openms/IDFilter.xml @@ -14,27 +14,27 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $whitelist.proteins: mkdir whitelist.proteins && - ln -s '$whitelist.proteins' 'whitelist.proteins/${re.sub("[^\w\-_]", "_", $whitelist.proteins.element_identifier)}.$gxy2omsext($whitelist.proteins.ext)' && + cp '$whitelist.proteins' 'whitelist.proteins/${re.sub("[^\w\-_]", "_", $whitelist.proteins.element_identifier)}.$gxy2omsext($whitelist.proteins.ext)' && #end if #if $whitelist.peptides: mkdir whitelist.peptides && - ln -s '$whitelist.peptides' 'whitelist.peptides/${re.sub("[^\w\-_]", "_", $whitelist.peptides.element_identifier)}.$gxy2omsext($whitelist.peptides.ext)' && + cp '$whitelist.peptides' 'whitelist.peptides/${re.sub("[^\w\-_]", "_", $whitelist.peptides.element_identifier)}.$gxy2omsext($whitelist.peptides.ext)' && #end if #if $blacklist.proteins: mkdir blacklist.proteins && - ln -s '$blacklist.proteins' 'blacklist.proteins/${re.sub("[^\w\-_]", "_", $blacklist.proteins.element_identifier)}.$gxy2omsext($blacklist.proteins.ext)' && + cp '$blacklist.proteins' 'blacklist.proteins/${re.sub("[^\w\-_]", "_", $blacklist.proteins.element_identifier)}.$gxy2omsext($blacklist.proteins.ext)' && #end if #if $blacklist.peptides: mkdir blacklist.peptides && - ln -s '$blacklist.peptides' 'blacklist.peptides/${re.sub("[^\w\-_]", "_", $blacklist.peptides.element_identifier)}.$gxy2omsext($blacklist.peptides.ext)' && + cp '$blacklist.peptides' 'blacklist.peptides/${re.sub("[^\w\-_]", "_", $blacklist.peptides.element_identifier)}.$gxy2omsext($blacklist.peptides.ext)' && #end if #if $in_silico_digestion.fasta: mkdir in_silico_digestion.fasta && - ln -s '$in_silico_digestion.fasta' 'in_silico_digestion.fasta/${re.sub("[^\w\-_]", "_", $in_silico_digestion.fasta.element_identifier)}.$gxy2omsext($in_silico_digestion.fasta.ext)' && + cp '$in_silico_digestion.fasta' 'in_silico_digestion.fasta/${re.sub("[^\w\-_]", "_", $in_silico_digestion.fasta.element_identifier)}.$gxy2omsext($in_silico_digestion.fasta.ext)' && #end if ## Main program call diff --git a/tools/openms/IDMapper.xml b/tools/openms/IDMapper.xml index 7087bcb9e..38068cf4a 100644 --- a/tools/openms/IDMapper.xml +++ b/tools/openms/IDMapper.xml @@ -14,13 +14,13 @@ ## Preprocessing mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $spectra._in: mkdir spectra.in && - ln -s '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' && + cp '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' && #end if ## Main program call diff --git a/tools/openms/IDMassAccuracy.xml b/tools/openms/IDMassAccuracy.xml index 83ed25754..e5f69c378 100644 --- a/tools/openms/IDMassAccuracy.xml +++ b/tools/openms/IDMassAccuracy.xml @@ -16,16 +16,16 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir id_in_cond.id_in && #if $id_in_cond.id_in_select == "no" mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} && -${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])} +${' '.join(["cp '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])} #else -ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' && +cp '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' && #end if #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_precursor && diff --git a/tools/openms/IDMerger.xml b/tools/openms/IDMerger.xml index a18e2a639..3d4741e0f 100644 --- a/tools/openms/IDMerger.xml +++ b/tools/openms/IDMerger.xml @@ -16,14 +16,14 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && #if $add_to: mkdir add_to && - ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' && + cp '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' && #end if ## Main program call diff --git a/tools/openms/IDPosteriorErrorProbability.xml b/tools/openms/IDPosteriorErrorProbability.xml index 75035cdf4..6186e4244 100644 --- a/tools/openms/IDPosteriorErrorProbability.xml +++ b/tools/openms/IDPosteriorErrorProbability.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_plot && diff --git a/tools/openms/IDRTCalibration.xml b/tools/openms/IDRTCalibration.xml index 337d053f9..d92eb6040 100644 --- a/tools/openms/IDRTCalibration.xml +++ b/tools/openms/IDRTCalibration.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/IDRipper.xml b/tools/openms/IDRipper.xml index 90ca61e40..091bcd5f8 100644 --- a/tools/openms/IDRipper.xml +++ b/tools/openms/IDRipper.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/IDScoreSwitcher.xml b/tools/openms/IDScoreSwitcher.xml index 95db5d272..977c425e8 100644 --- a/tools/openms/IDScoreSwitcher.xml +++ b/tools/openms/IDScoreSwitcher.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/IDSplitter.xml b/tools/openms/IDSplitter.xml index 2117d3725..67e35dee1 100644 --- a/tools/openms/IDSplitter.xml +++ b/tools/openms/IDSplitter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if diff --git a/tools/openms/InternalCalibration.xml b/tools/openms/InternalCalibration.xml index 1a49c5076..df265c019 100644 --- a/tools/openms/InternalCalibration.xml +++ b/tools/openms/InternalCalibration.xml @@ -14,15 +14,15 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $cal.id_in: mkdir cal.id_in && - ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' && + cp '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' && #end if #if $cal.lock_in: mkdir cal.lock_in && - ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' && + cp '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' && #end if #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir cal_lock_out && diff --git a/tools/openms/IsobaricAnalyzer.xml b/tools/openms/IsobaricAnalyzer.xml index 02688af94..7ba4e07ca 100644 --- a/tools/openms/IsobaricAnalyzer.xml +++ b/tools/openms/IsobaricAnalyzer.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/JSONExporter.xml b/tools/openms/JSONExporter.xml index bf7b308e1..58d7fdb1d 100644 --- a/tools/openms/JSONExporter.xml +++ b/tools/openms/JSONExporter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/LuciphorAdapter.xml b/tools/openms/LuciphorAdapter.xml index eb4b2430f..380a232b6 100644 --- a/tools/openms/LuciphorAdapter.xml +++ b/tools/openms/LuciphorAdapter.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MRMMapper.xml b/tools/openms/MRMMapper.xml index 45817f726..e9fc38a47 100644 --- a/tools/openms/MRMMapper.xml +++ b/tools/openms/MRMMapper.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MRMPairFinder.xml b/tools/openms/MRMPairFinder.xml index 701caf514..92b2549af 100644 --- a/tools/openms/MRMPairFinder.xml +++ b/tools/openms/MRMPairFinder.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir pair_in && -ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' && +cp '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' && mkdir out && #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir feature_out && diff --git a/tools/openms/MRMTransitionGroupPicker.xml b/tools/openms/MRMTransitionGroupPicker.xml index b319c0ede..867b9e632 100644 --- a/tools/openms/MRMTransitionGroupPicker.xml +++ b/tools/openms/MRMTransitionGroupPicker.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MSFraggerAdapter.xml b/tools/openms/MSFraggerAdapter.xml index 072c0abc1..2ea43405b 100644 --- a/tools/openms/MSFraggerAdapter.xml +++ b/tools/openms/MSFraggerAdapter.xml @@ -14,13 +14,13 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir opt_out && #end if mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && ## Main program call diff --git a/tools/openms/MSGFPlusAdapter.xml b/tools/openms/MSGFPlusAdapter.xml index 8da7c395e..7fc0a19e7 100644 --- a/tools/openms/MSGFPlusAdapter.xml +++ b/tools/openms/MSGFPlusAdapter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if @@ -22,10 +22,10 @@ ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($ mkdir mzid_out && #end if mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #if $conf: mkdir conf && - ln -s '$conf' 'conf/${re.sub("[^\w\-_]", "_", $conf.element_identifier)}.$gxy2omsext($conf.ext)' && + cp '$conf' 'conf/${re.sub("[^\w\-_]", "_", $conf.element_identifier)}.$gxy2omsext($conf.ext)' && #end if ## Main program call diff --git a/tools/openms/MSstatsConverter.xml b/tools/openms/MSstatsConverter.xml index f3550c222..a56e92f1d 100644 --- a/tools/openms/MSstatsConverter.xml +++ b/tools/openms/MSstatsConverter.xml @@ -14,18 +14,18 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir in_design && -ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && +cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && mkdir out && ## advanced options #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames && #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && - ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} + ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} #else - ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' && + cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' && #end if #end if diff --git a/tools/openms/MaRaClusterAdapter.xml b/tools/openms/MaRaClusterAdapter.xml index cf2f5985d..751646305 100644 --- a/tools/openms/MaRaClusterAdapter.xml +++ b/tools/openms/MaRaClusterAdapter.xml @@ -16,17 +16,17 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #if $id_in_cond.id_in: mkdir id_in_cond.id_in && #if $id_in_cond.id_in_select == "no" mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} && - ${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])} + ${' '.join(["cp '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])} #else - ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' && + cp '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' && #end if #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') diff --git a/tools/openms/MapAlignerIdentification.xml b/tools/openms/MapAlignerIdentification.xml index dba9e76b8..df073bc9a 100644 --- a/tools/openms/MapAlignerIdentification.xml +++ b/tools/openms/MapAlignerIdentification.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && @@ -30,11 +30,11 @@ ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_id #end if #if $design: mkdir design && - ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && + cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if #if $reference.file: mkdir reference.file && - ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' && + cp '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' && #end if ## Main program call diff --git a/tools/openms/MapAlignerPoseClustering.xml b/tools/openms/MapAlignerPoseClustering.xml index f0dd53415..36f8e80f9 100644 --- a/tools/openms/MapAlignerPoseClustering.xml +++ b/tools/openms/MapAlignerPoseClustering.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && @@ -30,7 +30,7 @@ ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_id #end if #if $reference.file: mkdir reference.file && - ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' && + cp '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' && #end if ## Main program call diff --git a/tools/openms/MapAlignerSpectrum.xml b/tools/openms/MapAlignerSpectrum.xml index 95a255827..cb4755e4d 100644 --- a/tools/openms/MapAlignerSpectrum.xml +++ b/tools/openms/MapAlignerSpectrum.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && diff --git a/tools/openms/MapAlignerTreeGuided.xml b/tools/openms/MapAlignerTreeGuided.xml index 77d699e12..4ee2ff20a 100644 --- a/tools/openms/MapAlignerTreeGuided.xml +++ b/tools/openms/MapAlignerTreeGuided.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && diff --git a/tools/openms/MapNormalizer.xml b/tools/openms/MapNormalizer.xml index cc403d6d6..a06222b59 100644 --- a/tools/openms/MapNormalizer.xml +++ b/tools/openms/MapNormalizer.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MapRTTransformer.xml b/tools/openms/MapRTTransformer.xml index cd78cd6fd..4f4562dc2 100644 --- a/tools/openms/MapRTTransformer.xml +++ b/tools/openms/MapRTTransformer.xml @@ -15,13 +15,13 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if mkdir trafo_in && -ln -s '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' && +cp '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' && #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir trafo_out && #end if diff --git a/tools/openms/MapStatistics.xml b/tools/openms/MapStatistics.xml index eb63b03c3..6b9f73276 100644 --- a/tools/openms/MapStatistics.xml +++ b/tools/openms/MapStatistics.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MascotAdapter.xml b/tools/openms/MascotAdapter.xml index d536a5603..4a8d24f29 100644 --- a/tools/openms/MascotAdapter.xml +++ b/tools/openms/MascotAdapter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MascotAdapterOnline.xml b/tools/openms/MascotAdapterOnline.xml index 47b8ffcbc..9e995e93e 100644 --- a/tools/openms/MascotAdapterOnline.xml +++ b/tools/openms/MascotAdapterOnline.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MassCalculator.xml b/tools/openms/MassCalculator.xml index 003fa640d..f158b0e92 100644 --- a/tools/openms/MassCalculator.xml +++ b/tools/openms/MassCalculator.xml @@ -15,7 +15,7 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && diff --git a/tools/openms/MassTraceExtractor.xml b/tools/openms/MassTraceExtractor.xml index bb125777b..02d8dfdf4 100644 --- a/tools/openms/MassTraceExtractor.xml +++ b/tools/openms/MassTraceExtractor.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MetaProSIP.xml b/tools/openms/MetaProSIP.xml index fb7e460d1..4d686581c 100644 --- a/tools/openms/MetaProSIP.xml +++ b/tools/openms/MetaProSIP.xml @@ -14,13 +14,13 @@ ## Preprocessing mkdir in_mzML && -ln -s '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' && +cp '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' && mkdir in_fasta && -ln -s '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' && +cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' && mkdir out_csv && mkdir out_peptide_centric_csv && mkdir in_featureXML && -ln -s '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' && +cp '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' && ## Main program call diff --git a/tools/openms/MetaboliteAdductDecharger.xml b/tools/openms/MetaboliteAdductDecharger.xml index f64ed094c..6cc2d84d5 100644 --- a/tools/openms/MetaboliteAdductDecharger.xml +++ b/tools/openms/MetaboliteAdductDecharger.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_cm && #end if diff --git a/tools/openms/MetaboliteSpectralMatcher.xml b/tools/openms/MetaboliteSpectralMatcher.xml index 9bdc10027..3a24e5848 100644 --- a/tools/openms/MetaboliteSpectralMatcher.xml +++ b/tools/openms/MetaboliteSpectralMatcher.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && mkdir out && #if "out_spectra_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_spectra && diff --git a/tools/openms/MultiplexResolver.xml b/tools/openms/MultiplexResolver.xml index 5e9c2f6a7..fa1d8283e 100644 --- a/tools/openms/MultiplexResolver.xml +++ b/tools/openms/MultiplexResolver.xml @@ -14,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $in_blacklist: mkdir in_blacklist && - ln -s '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' && + cp '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' && #end if mkdir out && #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',') diff --git a/tools/openms/MzMLSplitter.xml b/tools/openms/MzMLSplitter.xml index c6fd90b92..b88e9c55d 100644 --- a/tools/openms/MzMLSplitter.xml +++ b/tools/openms/MzMLSplitter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/MzTabExporter.xml b/tools/openms/MzTabExporter.xml index aac2f94ef..5711258e1 100644 --- a/tools/openms/MzTabExporter.xml +++ b/tools/openms/MzTabExporter.xml @@ -15,7 +15,7 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if mkdir out && diff --git a/tools/openms/NoiseFilterGaussian.xml b/tools/openms/NoiseFilterGaussian.xml index a08138952..a86ec47b3 100644 --- a/tools/openms/NoiseFilterGaussian.xml +++ b/tools/openms/NoiseFilterGaussian.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/NoiseFilterSGolay.xml b/tools/openms/NoiseFilterSGolay.xml index dc731551c..3c3a0ea27 100644 --- a/tools/openms/NoiseFilterSGolay.xml +++ b/tools/openms/NoiseFilterSGolay.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/NovorAdapter.xml b/tools/openms/NovorAdapter.xml index d903294ef..eb2e3b822 100644 --- a/tools/openms/NovorAdapter.xml +++ b/tools/openms/NovorAdapter.xml @@ -14,11 +14,11 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $novorFile: mkdir novorFile && - ln -s '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' && + cp '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' && #end if ## Main program call diff --git a/tools/openms/NucleicAcidSearchEngine.xml b/tools/openms/NucleicAcidSearchEngine.xml index ef5141bb8..0881c4797 100644 --- a/tools/openms/NucleicAcidSearchEngine.xml +++ b/tools/openms/NucleicAcidSearchEngine.xml @@ -14,14 +14,14 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $database: mkdir database && - ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && + cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #end if #if $digest: mkdir digest && - ln -s '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' && + cp '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' && #end if mkdir out && #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') diff --git a/tools/openms/OpenMSInfo.xml b/tools/openms/OpenMSInfo.xml index db987ff57..1dbcbb54b 100644 --- a/tools/openms/OpenMSInfo.xml +++ b/tools/openms/OpenMSInfo.xml @@ -16,7 +16,7 @@ ## advanced options #if $adv_opts.dummy: mkdir adv_opts.dummy && - ln -s '$adv_opts.dummy' 'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)' && + cp '$adv_opts.dummy' 'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)' && #end if diff --git a/tools/openms/OpenPepXL.xml b/tools/openms/OpenPepXL.xml index 4c0eb4900..28172b02d 100644 --- a/tools/openms/OpenPepXL.xml +++ b/tools/openms/OpenPepXL.xml @@ -14,11 +14,11 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir consensus && -ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' && +cp '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_idXML && #end if @@ -34,7 +34,7 @@ ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifi ## advanced options #if $adv_opts.decoy_database: mkdir adv_opts.decoy_database && - ln -s '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' && + cp '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' && #end if diff --git a/tools/openms/OpenPepXLLF.xml b/tools/openms/OpenPepXLLF.xml index 65728a747..985575d83 100644 --- a/tools/openms/OpenPepXLLF.xml +++ b/tools/openms/OpenPepXLLF.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_idXML && #end if @@ -32,7 +32,7 @@ ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifi ## advanced options #if $adv_opts.decoy_database: mkdir adv_opts.decoy_database && - ln -s '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' && + cp '$adv_opts.decoy_database' 'adv_opts.decoy_database/${re.sub("[^\w\-_]", "_", $adv_opts.decoy_database.element_identifier)}.$gxy2omsext($adv_opts.decoy_database.ext)' && #end if diff --git a/tools/openms/OpenSwathAnalyzer.xml b/tools/openms/OpenSwathAnalyzer.xml index 76fe4cb1f..aee74718c 100644 --- a/tools/openms/OpenSwathAnalyzer.xml +++ b/tools/openms/OpenSwathAnalyzer.xml @@ -14,21 +14,21 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && #if $rt_norm: mkdir rt_norm && - ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && + cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && #end if mkdir out && #if $swath_files_cond.swath_files: mkdir swath_files_cond.swath_files && #if $swath_files_cond.swath_files_select == "no" mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && - ${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])} + ${' '.join(["cp '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])} #else - ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' && + cp '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' && #end if #end if diff --git a/tools/openms/OpenSwathAssayGenerator.xml b/tools/openms/OpenSwathAssayGenerator.xml index a3b6f21af..6141c7d26 100644 --- a/tools/openms/OpenSwathAssayGenerator.xml +++ b/tools/openms/OpenSwathAssayGenerator.xml @@ -14,15 +14,15 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $swath_windows_file: mkdir swath_windows_file && - ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' && + cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' && #end if #if $unimod_file: mkdir unimod_file && - ln -s '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' && + cp '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' && #end if ## Main program call diff --git a/tools/openms/OpenSwathChromatogramExtractor.xml b/tools/openms/OpenSwathChromatogramExtractor.xml index f077aefcc..755027619 100644 --- a/tools/openms/OpenSwathChromatogramExtractor.xml +++ b/tools/openms/OpenSwathChromatogramExtractor.xml @@ -16,15 +16,15 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && #if $rt_norm: mkdir rt_norm && - ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && + cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && #end if mkdir out && diff --git a/tools/openms/OpenSwathConfidenceScoring.xml b/tools/openms/OpenSwathConfidenceScoring.xml index 03cc7b6a5..e9151b5d4 100644 --- a/tools/openms/OpenSwathConfidenceScoring.xml +++ b/tools/openms/OpenSwathConfidenceScoring.xml @@ -14,13 +14,13 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir lib && -ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && +cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && mkdir out && #if $trafo: mkdir trafo && - ln -s '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' && + cp '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' && #end if ## Main program call diff --git a/tools/openms/OpenSwathDIAPreScoring.xml b/tools/openms/OpenSwathDIAPreScoring.xml index 9d3a4a537..7e2e4a1c6 100644 --- a/tools/openms/OpenSwathDIAPreScoring.xml +++ b/tools/openms/OpenSwathDIAPreScoring.xml @@ -14,13 +14,13 @@ ## Preprocessing mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir swath_files_cond.swath_files && #if $swath_files_cond.swath_files_select == "no" mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && -${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])} +${' '.join(["cp '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])} #else -ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' && +cp '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' && #end if mkdir output_files && mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && diff --git a/tools/openms/OpenSwathDecoyGenerator.xml b/tools/openms/OpenSwathDecoyGenerator.xml index ff30d6c8b..1cc5d570b 100644 --- a/tools/openms/OpenSwathDecoyGenerator.xml +++ b/tools/openms/OpenSwathDecoyGenerator.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/OpenSwathFeatureXMLToTSV.xml b/tools/openms/OpenSwathFeatureXMLToTSV.xml index 087cda9cd..d45d15296 100644 --- a/tools/openms/OpenSwathFeatureXMLToTSV.xml +++ b/tools/openms/OpenSwathFeatureXMLToTSV.xml @@ -16,12 +16,12 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/OpenSwathFileSplitter.xml b/tools/openms/OpenSwathFileSplitter.xml index effbe857f..eabd79642 100644 --- a/tools/openms/OpenSwathFileSplitter.xml +++ b/tools/openms/OpenSwathFileSplitter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir outputDirectory && #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_qc && diff --git a/tools/openms/OpenSwathMzMLFileCacher.xml b/tools/openms/OpenSwathMzMLFileCacher.xml index ed684053e..1d9960a2b 100644 --- a/tools/openms/OpenSwathMzMLFileCacher.xml +++ b/tools/openms/OpenSwathMzMLFileCacher.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/OpenSwathRTNormalizer.xml b/tools/openms/OpenSwathRTNormalizer.xml index b8a8e40eb..78687a283 100644 --- a/tools/openms/OpenSwathRTNormalizer.xml +++ b/tools/openms/OpenSwathRTNormalizer.xml @@ -16,16 +16,16 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir out && #if $rt_norm: mkdir rt_norm && - ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && + cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && #end if ## Main program call diff --git a/tools/openms/OpenSwathRewriteToFeatureXML.xml b/tools/openms/OpenSwathRewriteToFeatureXML.xml index 697e50bc8..2c687454d 100644 --- a/tools/openms/OpenSwathRewriteToFeatureXML.xml +++ b/tools/openms/OpenSwathRewriteToFeatureXML.xml @@ -15,10 +15,10 @@ ## Preprocessing #if $csv: mkdir csv && - ln -s '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' && + cp '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' && #end if mkdir featureXML && -ln -s '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' && +cp '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/OpenSwathWorkflow.xml b/tools/openms/OpenSwathWorkflow.xml index cd5c2ee6c..d3aa9e2d9 100644 --- a/tools/openms/OpenSwathWorkflow.xml +++ b/tools/openms/OpenSwathWorkflow.xml @@ -14,20 +14,20 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && #if $tr_irt: mkdir tr_irt && - ln -s '$tr_irt' 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)' && + cp '$tr_irt' 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)' && #end if #if $tr_irt_nonlinear: mkdir tr_irt_nonlinear && - ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' && + cp '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' && #end if #if $swath_windows_file: mkdir swath_windows_file && - ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' && + cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' && #end if #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_features && @@ -53,7 +53,7 @@ ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($ ## advanced options #if $adv_opts.rt_norm: mkdir adv_opts.rt_norm && - ln -s '$adv_opts.rt_norm' 'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)' && + cp '$adv_opts.rt_norm' 'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)' && #end if diff --git a/tools/openms/PSMFeatureExtractor.xml b/tools/openms/PSMFeatureExtractor.xml index 615d61d7f..196b60dae 100644 --- a/tools/openms/PSMFeatureExtractor.xml +++ b/tools/openms/PSMFeatureExtractor.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && diff --git a/tools/openms/PeakPickerHiRes.xml b/tools/openms/PeakPickerHiRes.xml index f11ea8afe..1d1987471 100644 --- a/tools/openms/PeakPickerHiRes.xml +++ b/tools/openms/PeakPickerHiRes.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/PeakPickerIterative.xml b/tools/openms/PeakPickerIterative.xml index bf7c07f13..1011bcc79 100644 --- a/tools/openms/PeakPickerIterative.xml +++ b/tools/openms/PeakPickerIterative.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/PeakPickerWavelet.xml b/tools/openms/PeakPickerWavelet.xml index 7079edb23..2b8b5b412 100644 --- a/tools/openms/PeakPickerWavelet.xml +++ b/tools/openms/PeakPickerWavelet.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/PeptideIndexer.xml b/tools/openms/PeptideIndexer.xml index 3946b5aa0..508d20752 100644 --- a/tools/openms/PeptideIndexer.xml +++ b/tools/openms/PeptideIndexer.xml @@ -14,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $fasta: mkdir fasta && - ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && + cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && #end if mkdir out && diff --git a/tools/openms/PercolatorAdapter.xml b/tools/openms/PercolatorAdapter.xml index e3a86032d..2c4e9e049 100644 --- a/tools/openms/PercolatorAdapter.xml +++ b/tools/openms/PercolatorAdapter.xml @@ -17,23 +17,23 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && - ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} + ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else - ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && + cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #end if #if $in_decoy_cond.in_decoy: mkdir in_decoy_cond.in_decoy && #if $in_decoy_cond.in_decoy_select == "no" mkdir ${' '.join(["'in_decoy_cond.in_decoy/%s'" % (i) for i, f in enumerate($in_decoy_cond.in_decoy) if f])} && - ${' '.join(["ln -s '%s' 'in_decoy_cond.in_decoy/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])} + ${' '.join(["cp '%s' 'in_decoy_cond.in_decoy/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_decoy_cond.in_decoy) if f])} #else - ln -s '$in_decoy_cond.in_decoy' 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)' && + cp '$in_decoy_cond.in_decoy' 'in_decoy_cond.in_decoy/${re.sub("[^\w\-_]", "_", $in_decoy_cond.in_decoy.element_identifier)}.$gxy2omsext($in_decoy_cond.in_decoy.ext)' && #end if #end if #if $in_osw: mkdir in_osw && - ln -s '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' && + cp '$in_osw' 'in_osw/${re.sub("[^\w\-_]", "_", $in_osw.element_identifier)}.$gxy2omsext($in_osw.ext)' && #end if mkdir out && #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') @@ -57,11 +57,11 @@ mkdir out && ## advanced options #if $adv_opts.init_weights: mkdir adv_opts.init_weights && - ln -s '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' && + cp '$adv_opts.init_weights' 'adv_opts.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts.init_weights.element_identifier)}.$gxy2omsext($adv_opts.init_weights.ext)' && #end if #if $adv_opts.fasta: mkdir adv_opts.fasta && - ln -s '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' && + cp '$adv_opts.fasta' 'adv_opts.fasta/${re.sub("[^\w\-_]", "_", $adv_opts.fasta.element_identifier)}.$gxy2omsext($adv_opts.fasta.ext)' && #end if diff --git a/tools/openms/PhosphoScoring.xml b/tools/openms/PhosphoScoring.xml index 5b32269b2..57641810d 100644 --- a/tools/openms/PhosphoScoring.xml +++ b/tools/openms/PhosphoScoring.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir id && -ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/PrecursorMassCorrector.xml b/tools/openms/PrecursorMassCorrector.xml index d1c8de035..984dc528e 100644 --- a/tools/openms/PrecursorMassCorrector.xml +++ b/tools/openms/PrecursorMassCorrector.xml @@ -14,11 +14,11 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $feature_in: mkdir feature_in && - ln -s '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' && + cp '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' && #end if ## Main program call diff --git a/tools/openms/ProteinInference.xml b/tools/openms/ProteinInference.xml index 56ca8551d..53ba89e25 100644 --- a/tools/openms/ProteinInference.xml +++ b/tools/openms/ProteinInference.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && diff --git a/tools/openms/ProteinQuantifier.xml b/tools/openms/ProteinQuantifier.xml index 459defe5d..14153054f 100644 --- a/tools/openms/ProteinQuantifier.xml +++ b/tools/openms/ProteinQuantifier.xml @@ -14,14 +14,14 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $protein_groups: mkdir protein_groups && - ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' && + cp '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' && #end if #if $design: mkdir design && - ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && + cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && diff --git a/tools/openms/ProteinResolver.xml b/tools/openms/ProteinResolver.xml index 08f58dbfd..132ca29c8 100644 --- a/tools/openms/ProteinResolver.xml +++ b/tools/openms/ProteinResolver.xml @@ -14,19 +14,19 @@ ## Preprocessing mkdir fasta && -ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && +cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && #if $in_cond.in: mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && - ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} + ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else - ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && + cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if #end if #if $design: mkdir design && - ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && + cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir protein_groups && diff --git a/tools/openms/QCCalculator.xml b/tools/openms/QCCalculator.xml index 4e221be6c..1e1327bed 100644 --- a/tools/openms/QCCalculator.xml +++ b/tools/openms/QCCalculator.xml @@ -14,19 +14,19 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $id: mkdir id && - ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && + cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && #end if #if $feature: mkdir feature && - ln -s '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' && + cp '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' && #end if #if $consensus: mkdir consensus && - ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' && + cp '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' && #end if ## Main program call diff --git a/tools/openms/QCEmbedder.xml b/tools/openms/QCEmbedder.xml index 6a6a49136..7d03792e8 100644 --- a/tools/openms/QCEmbedder.xml +++ b/tools/openms/QCEmbedder.xml @@ -15,19 +15,19 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if #if $run: mkdir run && - ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && + cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && #end if #if $plot: mkdir plot && - ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' && + cp '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' && #end if #if $table: mkdir table && - ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' && + cp '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' && #end if mkdir out && diff --git a/tools/openms/QCExporter.xml b/tools/openms/QCExporter.xml index 3d6cbe0a5..a7e79b82c 100644 --- a/tools/openms/QCExporter.xml +++ b/tools/openms/QCExporter.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir mapping && -ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' && +cp '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' && mkdir out_csv && ## Main program call diff --git a/tools/openms/QCExtractor.xml b/tools/openms/QCExtractor.xml index 14ea7c804..fee26e75a 100644 --- a/tools/openms/QCExtractor.xml +++ b/tools/openms/QCExtractor.xml @@ -14,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $run: mkdir run && - ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && + cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && #end if mkdir out_csv && diff --git a/tools/openms/QCImporter.xml b/tools/openms/QCImporter.xml index 22833a8b3..219ea7a9a 100644 --- a/tools/openms/QCImporter.xml +++ b/tools/openms/QCImporter.xml @@ -15,12 +15,12 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if mkdir table && -ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' && +cp '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' && mkdir mapping && -ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' && +cp '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/QCMerger.xml b/tools/openms/QCMerger.xml index 773bc891c..c2d937ee7 100644 --- a/tools/openms/QCMerger.xml +++ b/tools/openms/QCMerger.xml @@ -16,9 +16,9 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && diff --git a/tools/openms/QCShrinker.xml b/tools/openms/QCShrinker.xml index f00098b81..979ef40f5 100644 --- a/tools/openms/QCShrinker.xml +++ b/tools/openms/QCShrinker.xml @@ -14,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $run: mkdir run && - ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && + cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && #end if mkdir out && diff --git a/tools/openms/QualityControl.xml b/tools/openms/QualityControl.xml index 8dec7c125..7b5968eaa 100644 --- a/tools/openms/QualityControl.xml +++ b/tools/openms/QualityControl.xml @@ -14,23 +14,23 @@ ## Preprocessing mkdir in_cm && -ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' && +cp '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' && #if $in_raw_cond.in_raw: mkdir in_raw_cond.in_raw && #if $in_raw_cond.in_raw_select == "no" mkdir ${' '.join(["'in_raw_cond.in_raw/%s'" % (i) for i, f in enumerate($in_raw_cond.in_raw) if f])} && - ${' '.join(["ln -s '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])} + ${' '.join(["cp '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])} #else - ln -s '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' && + cp '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' && #end if #end if #if $in_postFDR_cond.in_postFDR: mkdir in_postFDR_cond.in_postFDR && #if $in_postFDR_cond.in_postFDR_select == "no" mkdir ${' '.join(["'in_postFDR_cond.in_postFDR/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} && - ${' '.join(["ln -s '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} + ${' '.join(["cp '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} #else - ln -s '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' && + cp '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' && #end if #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') @@ -45,19 +45,19 @@ ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy #end if #if $in_contaminants: mkdir in_contaminants && - ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' && + cp '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' && #end if #if $in_fasta: mkdir in_fasta && - ln -s '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' && + cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' && #end if #if $in_trafo_cond.in_trafo: mkdir in_trafo_cond.in_trafo && #if $in_trafo_cond.in_trafo_select == "no" mkdir ${' '.join(["'in_trafo_cond.in_trafo/%s'" % (i) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} && - ${' '.join(["ln -s '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} + ${' '.join(["cp '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} #else - ln -s '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' && + cp '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' && #end if #end if diff --git a/tools/openms/RNADigestor.xml b/tools/openms/RNADigestor.xml index a7586b19c..b5c3b971c 100644 --- a/tools/openms/RNADigestor.xml +++ b/tools/openms/RNADigestor.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/RNAMassCalculator.xml b/tools/openms/RNAMassCalculator.xml index a8cb48a23..53876282b 100644 --- a/tools/openms/RNAMassCalculator.xml +++ b/tools/openms/RNAMassCalculator.xml @@ -15,7 +15,7 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && diff --git a/tools/openms/RNPxlSearch.xml b/tools/openms/RNPxlSearch.xml index 38730ce32..7263fa995 100644 --- a/tools/openms/RNPxlSearch.xml +++ b/tools/openms/RNPxlSearch.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && mkdir out && #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_tsv && diff --git a/tools/openms/RNPxlXICFilter.xml b/tools/openms/RNPxlXICFilter.xml index aa623bdcf..7b0c5f679 100644 --- a/tools/openms/RNPxlXICFilter.xml +++ b/tools/openms/RNPxlXICFilter.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir control && -ln -s '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' && +cp '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' && mkdir treatment && -ln -s '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' && +cp '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SageAdapter.xml b/tools/openms/SageAdapter.xml index 6260805e0..93ce05f95 100644 --- a/tools/openms/SageAdapter.xml +++ b/tools/openms/SageAdapter.xml @@ -16,13 +16,13 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && ## Main program call diff --git a/tools/openms/SeedListGenerator.xml b/tools/openms/SeedListGenerator.xml index 3f25f39f2..60aa75299 100644 --- a/tools/openms/SeedListGenerator.xml +++ b/tools/openms/SeedListGenerator.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out_prefix && ## Main program call diff --git a/tools/openms/SemanticValidator.xml b/tools/openms/SemanticValidator.xml index b495bc887..91939a3d4 100644 --- a/tools/openms/SemanticValidator.xml +++ b/tools/openms/SemanticValidator.xml @@ -14,16 +14,16 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir mapping_file && -ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && +cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && #if $cv_cond.cv: mkdir cv_cond.cv && #if $cv_cond.cv_select == "no" mkdir ${' '.join(["'cv_cond.cv/%s'" % (i) for i, f in enumerate($cv_cond.cv) if f])} && - ${' '.join(["ln -s '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])} + ${' '.join(["cp '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])} #else - ln -s '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' && + cp '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' && #end if #end if diff --git a/tools/openms/SequenceCoverageCalculator.xml b/tools/openms/SequenceCoverageCalculator.xml index c564c0a6f..3f1ea939d 100644 --- a/tools/openms/SequenceCoverageCalculator.xml +++ b/tools/openms/SequenceCoverageCalculator.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in_database && -ln -s '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' && +cp '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' && mkdir in_peptides && -ln -s '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' && +cp '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SimpleSearchEngine.xml b/tools/openms/SimpleSearchEngine.xml index 336024aee..d39cfecf3 100644 --- a/tools/openms/SimpleSearchEngine.xml +++ b/tools/openms/SimpleSearchEngine.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SiriusAdapter.xml b/tools/openms/SiriusAdapter.xml index f03e73d6c..62d5e1c7b 100644 --- a/tools/openms/SiriusAdapter.xml +++ b/tools/openms/SiriusAdapter.xml @@ -14,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $in_featureinfo: mkdir in_featureinfo && - ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' && + cp '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' && #end if #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_sirius && diff --git a/tools/openms/SpecLibCreator.xml b/tools/openms/SpecLibCreator.xml index 6e4cf63c5..2e54224ca 100644 --- a/tools/openms/SpecLibCreator.xml +++ b/tools/openms/SpecLibCreator.xml @@ -14,9 +14,9 @@ ## Preprocessing mkdir info && -ln -s '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' && +cp '$info' 'info/${re.sub("[^\w\-_]", "_", $info.element_identifier)}.$gxy2omsext($info.ext)' && mkdir spec && -ln -s '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' && +cp '$spec' 'spec/${re.sub("[^\w\-_]", "_", $spec.element_identifier)}.$gxy2omsext($spec.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpecLibSearcher.xml b/tools/openms/SpecLibSearcher.xml index 09d4e12e4..55ae0544f 100644 --- a/tools/openms/SpecLibSearcher.xml +++ b/tools/openms/SpecLibSearcher.xml @@ -16,12 +16,12 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir lib && -ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && +cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && mkdir out && mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && diff --git a/tools/openms/SpectraFilterBernNorm.xml b/tools/openms/SpectraFilterBernNorm.xml index f7a91b23a..dea23e2c3 100644 --- a/tools/openms/SpectraFilterBernNorm.xml +++ b/tools/openms/SpectraFilterBernNorm.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterMarkerMower.xml b/tools/openms/SpectraFilterMarkerMower.xml index 9be6dffe3..245b2dda0 100644 --- a/tools/openms/SpectraFilterMarkerMower.xml +++ b/tools/openms/SpectraFilterMarkerMower.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterNLargest.xml b/tools/openms/SpectraFilterNLargest.xml index 26d7d00ee..e344604d4 100644 --- a/tools/openms/SpectraFilterNLargest.xml +++ b/tools/openms/SpectraFilterNLargest.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterNormalizer.xml b/tools/openms/SpectraFilterNormalizer.xml index 6e32a1400..ce6fa07ec 100644 --- a/tools/openms/SpectraFilterNormalizer.xml +++ b/tools/openms/SpectraFilterNormalizer.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterParentPeakMower.xml b/tools/openms/SpectraFilterParentPeakMower.xml index 5588aad13..4b8dec0f7 100644 --- a/tools/openms/SpectraFilterParentPeakMower.xml +++ b/tools/openms/SpectraFilterParentPeakMower.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterScaler.xml b/tools/openms/SpectraFilterScaler.xml index e1d40bf58..832843831 100644 --- a/tools/openms/SpectraFilterScaler.xml +++ b/tools/openms/SpectraFilterScaler.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterSqrtMower.xml b/tools/openms/SpectraFilterSqrtMower.xml index 52e36adb0..0b6112da1 100644 --- a/tools/openms/SpectraFilterSqrtMower.xml +++ b/tools/openms/SpectraFilterSqrtMower.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterThresholdMower.xml b/tools/openms/SpectraFilterThresholdMower.xml index 0a80f4cec..b26c465b5 100644 --- a/tools/openms/SpectraFilterThresholdMower.xml +++ b/tools/openms/SpectraFilterThresholdMower.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraFilterWindowMower.xml b/tools/openms/SpectraFilterWindowMower.xml index 7f4b2cff8..4a6e5f42e 100644 --- a/tools/openms/SpectraFilterWindowMower.xml +++ b/tools/openms/SpectraFilterWindowMower.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraMerger.xml b/tools/openms/SpectraMerger.xml index 5af9e061a..da5ecf9d2 100644 --- a/tools/openms/SpectraMerger.xml +++ b/tools/openms/SpectraMerger.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/SpectraSTSearchAdapter.xml b/tools/openms/SpectraSTSearchAdapter.xml index 8b38d797a..a5e18d854 100644 --- a/tools/openms/SpectraSTSearchAdapter.xml +++ b/tools/openms/SpectraSTSearchAdapter.xml @@ -16,26 +16,26 @@ mkdir spectra_files_cond.spectra_files && #if $spectra_files_cond.spectra_files_select == "no" mkdir ${' '.join(["'spectra_files_cond.spectra_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && -${' '.join(["ln -s '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} +${' '.join(["cp '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} #else -ln -s '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' && +cp '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' && #end if mkdir output_files && mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && mkdir library_file && -ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' && +cp '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' && #if $sequence_database_file: mkdir sequence_database_file && - ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' && + cp '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' && #end if #if $search_file: mkdir search_file && - ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' && + cp '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' && #end if ## advanced options #if $adv_opts.user_mod_file: mkdir adv_opts.user_mod_file && - ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' && + cp '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' && #end if diff --git a/tools/openms/StaticModification.xml b/tools/openms/StaticModification.xml index 1dcbce5b9..d9cc734de 100644 --- a/tools/openms/StaticModification.xml +++ b/tools/openms/StaticModification.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/TICCalculator.xml b/tools/openms/TICCalculator.xml index bc9e90f4f..feaca4d6d 100644 --- a/tools/openms/TICCalculator.xml +++ b/tools/openms/TICCalculator.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && ## Main program call diff --git a/tools/openms/TOFCalibration.xml b/tools/openms/TOFCalibration.xml index 0f1788900..de1f3d791 100644 --- a/tools/openms/TOFCalibration.xml +++ b/tools/openms/TOFCalibration.xml @@ -14,14 +14,14 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && mkdir ext_calibrants && -ln -s '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' && +cp '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' && mkdir ref_masses && -ln -s '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' && +cp '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' && mkdir tof_const && -ln -s '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' && +cp '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' && ## Main program call diff --git a/tools/openms/TargetedFileConverter.xml b/tools/openms/TargetedFileConverter.xml index e29fcd262..15f1af683 100644 --- a/tools/openms/TargetedFileConverter.xml +++ b/tools/openms/TargetedFileConverter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call diff --git a/tools/openms/TextExporter.xml b/tools/openms/TextExporter.xml index 99915e17e..a0ba7b927 100644 --- a/tools/openms/TextExporter.xml +++ b/tools/openms/TextExporter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir consensus_centroids && diff --git a/tools/openms/TriqlerConverter.xml b/tools/openms/TriqlerConverter.xml index 7151a03f0..7955889b9 100644 --- a/tools/openms/TriqlerConverter.xml +++ b/tools/openms/TriqlerConverter.xml @@ -14,18 +14,18 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir in_design && -ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && +cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && mkdir out && ## advanced options #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames && #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && - ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} + ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} #else - ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' && + cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' && #end if #end if diff --git a/tools/openms/XFDR.xml b/tools/openms/XFDR.xml index d6d2363de..ec7b7e59d 100644 --- a/tools/openms/XFDR.xml +++ b/tools/openms/XFDR.xml @@ -15,7 +15,7 @@ ## Preprocessing #if $in: mkdir in && - ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if #if "out_idXML_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_idXML && diff --git a/tools/openms/XMLValidator.xml b/tools/openms/XMLValidator.xml index f4fd0ae2e..9031f9fe3 100644 --- a/tools/openms/XMLValidator.xml +++ b/tools/openms/XMLValidator.xml @@ -14,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $schema: mkdir schema && - ln -s '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' && + cp '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' && #end if ## Main program call diff --git a/tools/openms/XTandemAdapter.xml b/tools/openms/XTandemAdapter.xml index b22067767..faa0f1ae7 100644 --- a/tools/openms/XTandemAdapter.xml +++ b/tools/openms/XTandemAdapter.xml @@ -14,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if @@ -22,10 +22,10 @@ ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($ mkdir xml_out && #end if mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #if $default_config_file: mkdir default_config_file && - ln -s '$default_config_file' 'default_config_file/${re.sub("[^\w\-_]", "_", $default_config_file.element_identifier)}.$gxy2omsext($default_config_file.ext)' && + cp '$default_config_file' 'default_config_file/${re.sub("[^\w\-_]", "_", $default_config_file.element_identifier)}.$gxy2omsext($default_config_file.ext)' && #end if ## Main program call