From fd8160798d3a3e03783467ecb0bf1cfc8e71ddf2 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Fri, 14 Jun 2024 19:12:08 +0200 Subject: [PATCH] omit optional if default --- tools/openms/AccurateMassSearch.xml | 18 +-- tools/openms/AssayGeneratorMetabo.xml | 98 ++++++------ tools/openms/BaselineFilter.xml | 10 +- tools/openms/CVInspector.xml | 12 +- tools/openms/ClusterMassTraces.xml | 16 +- tools/openms/ClusterMassTracesByPrecursor.xml | 18 +-- tools/openms/CometAdapter.xml | 80 +++++----- tools/openms/ConsensusID.xml | 24 +-- tools/openms/ConsensusMapNormalizer.xml | 8 +- tools/openms/DTAExtractor.xml | 12 +- tools/openms/DatabaseFilter.xml | 8 +- tools/openms/DatabaseSuitability.xml | 20 +-- tools/openms/DeMeanderize.xml | 8 +- tools/openms/DecoyDatabase.xml | 22 +-- tools/openms/Digestor.xml | 19 +-- tools/openms/DigestorMotif.xml | 16 +- tools/openms/EICExtractor.xml | 22 +-- tools/openms/ERPairFinder.xml | 18 +-- tools/openms/Epifany.xml | 41 ++--- tools/openms/ExternalCalibration.xml | 12 +- tools/openms/FalseDiscoveryRate.xml | 8 +- tools/openms/FeatureFinderCentroided.xml | 60 ++++---- tools/openms/FeatureFinderIdentification.xml | 64 ++++---- tools/openms/FeatureFinderIsotopeWavelet.xml | 14 +- tools/openms/FeatureFinderMRM.xml | 10 +- tools/openms/FeatureFinderMetabo.xml | 42 ++--- tools/openms/FeatureFinderMetaboIdent.xml | 34 ++-- tools/openms/FeatureFinderMultiplex.xml | 62 ++++---- tools/openms/FeatureLinkerLabeled.xml | 14 +- tools/openms/FeatureLinkerUnlabeled.xml | 28 ++-- tools/openms/FeatureLinkerUnlabeledKD.xml | 52 +++---- tools/openms/FeatureLinkerUnlabeledQT.xml | 34 ++-- tools/openms/FileConverter.xml | 13 +- tools/openms/FileFilter.xml | 81 +++++----- tools/openms/FileInfo.xml | 4 +- tools/openms/FileMerger.xml | 14 +- tools/openms/FuzzyDiff.xml | 18 +-- tools/openms/GNPSExport.xml | 16 +- .../openms/HighResPrecursorMassCorrector.xml | 20 +-- tools/openms/IDConflictResolver.xml | 6 +- tools/openms/IDExtractor.xml | 8 +- tools/openms/IDFileConverter.xml | 49 +++--- tools/openms/IDFilter.xml | 50 +++--- tools/openms/IDMapper.xml | 14 +- tools/openms/IDMassAccuracy.xml | 14 +- tools/openms/IDMerger.xml | 9 +- tools/openms/IDPosteriorErrorProbability.xml | 16 +- tools/openms/IDRTCalibration.xml | 12 +- tools/openms/IDRipper.xml | 4 +- tools/openms/IDScoreSwitcher.xml | 4 +- tools/openms/IDSplitter.xml | 4 +- tools/openms/InternalCalibration.xml | 22 +-- tools/openms/IsobaricAnalyzer.xml | 46 +++--- tools/openms/JSONExporter.xml | 4 +- tools/openms/LuciphorAdapter.xml | 38 ++--- tools/openms/MRMMapper.xml | 10 +- tools/openms/MRMPairFinder.xml | 12 +- tools/openms/MRMTransitionGroupPicker.xml | 44 +++--- tools/openms/MSFraggerAdapter.xml | 145 +++++++++--------- tools/openms/MSGFPlusAdapter.xml | 56 +++---- tools/openms/MSstatsConverter.xml | 18 +-- tools/openms/MapAlignerIdentification.xml | 50 +++--- tools/openms/MapAlignerPoseClustering.xml | 46 +++--- tools/openms/MapAlignerSpectrum.xml | 56 +++---- tools/openms/MapAlignerTreeGuided.xml | 50 +++--- tools/openms/MapNormalizer.xml | 4 +- tools/openms/MapRTTransformer.xml | 40 ++--- tools/openms/MapStatistics.xml | 6 +- tools/openms/MascotAdapter.xml | 45 +++--- tools/openms/MascotAdapterOnline.xml | 54 +++---- tools/openms/MassCalculator.xml | 8 +- tools/openms/MassTraceExtractor.xml | 33 ++-- tools/openms/MetaProSIP.xml | 48 +++--- tools/openms/MetaboliteSpectralMatcher.xml | 16 +- tools/openms/MultiplexResolver.xml | 42 ++--- tools/openms/MzMLSplitter.xml | 10 +- tools/openms/MzTabExporter.xml | 4 +- tools/openms/NoiseFilterGaussian.xml | 10 +- tools/openms/NoiseFilterSGolay.xml | 10 +- tools/openms/NovorAdapter.xml | 22 +-- tools/openms/NucleicAcidSearchEngine.xml | 38 ++--- tools/openms/OpenMSDatabasesInfo.xml | 2 +- tools/openms/OpenMSInfo.xml | 2 +- tools/openms/OpenPepXL.xml | 54 +++---- tools/openms/OpenPepXLLF.xml | 52 +++---- tools/openms/OpenSwathAnalyzer.xml | 96 ++++++------ tools/openms/OpenSwathAssayGenerator.xml | 29 ++-- .../openms/OpenSwathChromatogramExtractor.xml | 20 +-- tools/openms/OpenSwathConfidenceScoring.xml | 16 +- tools/openms/OpenSwathDIAPreScoring.xml | 10 +- tools/openms/OpenSwathDecoyGenerator.xml | 29 ++-- tools/openms/OpenSwathFeatureXMLToTSV.xml | 8 +- tools/openms/OpenSwathFileSplitter.xml | 4 +- tools/openms/OpenSwathMzMLFileCacher.xml | 11 +- tools/openms/OpenSwathRTNormalizer.xml | 114 +++++++------- tools/openms/OpenSwathRewriteToFeatureXML.xml | 6 +- tools/openms/OpenSwathWorkflow.xml | 142 ++++++++--------- tools/openms/PSMFeatureExtractor.xml | 9 +- tools/openms/PeakPickerHiRes.xml | 32 ++-- tools/openms/PeakPickerIterative.xml | 16 +- tools/openms/PeakPickerWavelet.xml | 82 +++++----- tools/openms/PeptideIndexer.xml | 18 +-- tools/openms/PercolatorAdapter.xml | 43 +++--- tools/openms/PhosphoScoring.xml | 16 +- tools/openms/PrecursorMassCorrector.xml | 10 +- tools/openms/ProteinInference.xml | 17 +- tools/openms/ProteinQuantifier.xml | 14 +- tools/openms/ProteinResolver.xml | 18 +-- tools/openms/QCCalculator.xml | 9 +- tools/openms/QCEmbedder.xml | 4 +- tools/openms/QCExporter.xml | 6 +- tools/openms/QCExtractor.xml | 6 +- tools/openms/QCImporter.xml | 6 +- tools/openms/QCMerger.xml | 6 +- tools/openms/QCShrinker.xml | 4 +- tools/openms/QualityControl.xml | 14 +- tools/openms/RNADigestor.xml | 12 +- tools/openms/RNAMassCalculator.xml | 8 +- tools/openms/RNPxlSearch.xml | 54 +++---- tools/openms/RNPxlXICFilter.xml | 12 +- tools/openms/SageAdapter.xml | 76 ++++----- tools/openms/SeedListGenerator.xml | 4 +- tools/openms/SemanticValidator.xml | 8 +- tools/openms/SequenceCoverageCalculator.xml | 6 +- tools/openms/SimpleSearchEngine.xml | 38 ++--- tools/openms/SiriusAdapter.xml | 40 ++--- tools/openms/SpecLibCreator.xml | 8 +- tools/openms/SpecLibSearcher.xml | 38 ++--- tools/openms/SpectraFilterBernNorm.xml | 10 +- tools/openms/SpectraFilterMarkerMower.xml | 4 +- tools/openms/SpectraFilterNLargest.xml | 6 +- tools/openms/SpectraFilterNormalizer.xml | 6 +- tools/openms/SpectraFilterParentPeakMower.xml | 20 +-- tools/openms/SpectraFilterScaler.xml | 4 +- tools/openms/SpectraFilterSqrtMower.xml | 4 +- tools/openms/SpectraFilterThresholdMower.xml | 6 +- tools/openms/SpectraFilterWindowMower.xml | 10 +- tools/openms/SpectraMerger.xml | 44 +++--- tools/openms/SpectraSTSearchAdapter.xml | 14 +- tools/openms/StaticModification.xml | 8 +- tools/openms/TICCalculator.xml | 6 +- tools/openms/TOFCalibration.xml | 88 +++++------ tools/openms/TargetedFileConverter.xml | 9 +- tools/openms/TextExporter.xml | 21 +-- tools/openms/TriqlerConverter.xml | 10 +- tools/openms/XFDR.xml | 16 +- tools/openms/XMLValidator.xml | 4 +- tools/openms/XTandemAdapter.xml | 44 +++--- 148 files changed, 1914 insertions(+), 1896 deletions(-) diff --git a/tools/openms/AccurateMassSearch.xml b/tools/openms/AccurateMassSearch.xml index f2413333c..4f7d59a47 100644 --- a/tools/openms/AccurateMassSearch.xml +++ b/tools/openms/AccurateMassSearch.xml @@ -101,8 +101,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -119,7 +119,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -131,18 +131,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - + + - + @@ -151,7 +151,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -162,7 +162,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/AssayGeneratorMetabo.xml b/tools/openms/AssayGeneratorMetabo.xml index 2d09e35bb..0257cf7ca 100644 --- a/tools/openms/AssayGeneratorMetabo.xml +++ b/tools/openms/AssayGeneratorMetabo.xml @@ -66,10 +66,10 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_ - + - + @@ -78,79 +78,79 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_ - + - + - + - + - - - - + + + + - + - + - - + + - - - - + + + +
- - + + - - - - + + + +
- - - + + + - - + +
- - + + @@ -158,12 +158,12 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_
- - - - + + + + - + @@ -176,23 +176,23 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_ - - - + + + - + - + - + - +
@@ -202,22 +202,22 @@ ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_ - + - - + + - - + + - + diff --git a/tools/openms/BaselineFilter.xml b/tools/openms/BaselineFilter.xml index 0693c09a1..334e7a5e5 100644 --- a/tools/openms/BaselineFilter.xml +++ b/tools/openms/BaselineFilter.xml @@ -38,14 +38,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - + @@ -60,7 +60,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/CVInspector.xml b/tools/openms/CVInspector.xml index af8c3210d..7c49058a2 100644 --- a/tools/openms/CVInspector.xml +++ b/tools/openms/CVInspector.xml @@ -66,24 +66,24 @@ ${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.el - + - + - + - - + + - + diff --git a/tools/openms/ClusterMassTraces.xml b/tools/openms/ClusterMassTraces.xml index 1b3fda50d..1f9931452 100644 --- a/tools/openms/ClusterMassTraces.xml +++ b/tools/openms/ClusterMassTraces.xml @@ -38,16 +38,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - - + + + + + + + - + diff --git a/tools/openms/ClusterMassTracesByPrecursor.xml b/tools/openms/ClusterMassTracesByPrecursor.xml index f1a0139a7..3d1976c85 100644 --- a/tools/openms/ClusterMassTracesByPrecursor.xml +++ b/tools/openms/ClusterMassTracesByPrecursor.xml @@ -42,18 +42,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - - - - - + + + + + + - + diff --git a/tools/openms/CometAdapter.xml b/tools/openms/CometAdapter.xml index cafe858de..87d95f443 100644 --- a/tools/openms/CometAdapter.xml +++ b/tools/openms/CometAdapter.xml @@ -63,17 +63,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - + + - + @@ -82,18 +82,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - + + - + @@ -108,29 +108,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - - - - + + + + + - + - - + + @@ -140,9 +140,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -3109,7 +3109,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6084,12 +6084,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -6098,18 +6098,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - + +
- + @@ -6146,7 +6146,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6178,31 +6178,31 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - - + + + - - - + + + - - + + - + - + diff --git a/tools/openms/ConsensusID.xml b/tools/openms/ConsensusID.xml index 77e0f88b9..a4309241a 100644 --- a/tools/openms/ConsensusID.xml +++ b/tools/openms/ConsensusID.xml @@ -53,16 +53,16 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - - + + - + @@ -72,26 +72,26 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- - + +
- - + +
- + - +
- + diff --git a/tools/openms/ConsensusMapNormalizer.xml b/tools/openms/ConsensusMapNormalizer.xml index 5078c34bb..31d77d83b 100644 --- a/tools/openms/ConsensusMapNormalizer.xml +++ b/tools/openms/ConsensusMapNormalizer.xml @@ -38,15 +38,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + @@ -55,7 +55,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/DTAExtractor.xml b/tools/openms/DTAExtractor.xml index 4f2d99237..3232b31d9 100644 --- a/tools/openms/DTAExtractor.xml +++ b/tools/openms/DTAExtractor.xml @@ -35,22 +35,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + - + - + - + diff --git a/tools/openms/DatabaseFilter.xml b/tools/openms/DatabaseFilter.xml index 2ebe231c2..0a1d712ef 100644 --- a/tools/openms/DatabaseFilter.xml +++ b/tools/openms/DatabaseFilter.xml @@ -42,16 +42,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - + diff --git a/tools/openms/DatabaseSuitability.xml b/tools/openms/DatabaseSuitability.xml index 4c0397beb..f255fabfe 100644 --- a/tools/openms/DatabaseSuitability.xml +++ b/tools/openms/DatabaseSuitability.xml @@ -63,24 +63,24 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - + + + + +
- - - + + +
- + - + diff --git a/tools/openms/DeMeanderize.xml b/tools/openms/DeMeanderize.xml index d5b35b0f4..b57c9867b 100644 --- a/tools/openms/DeMeanderize.xml +++ b/tools/openms/DeMeanderize.xml @@ -38,12 +38,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + - + diff --git a/tools/openms/DecoyDatabase.xml b/tools/openms/DecoyDatabase.xml index b56a97b05..8837e991e 100644 --- a/tools/openms/DecoyDatabase.xml +++ b/tools/openms/DecoyDatabase.xml @@ -53,32 +53,32 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + - + - + - + - + @@ -122,13 +122,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- - - + + + - + diff --git a/tools/openms/Digestor.xml b/tools/openms/Digestor.xml index 68caa575b..5acffe865 100644 --- a/tools/openms/Digestor.xml +++ b/tools/openms/Digestor.xml @@ -38,16 +38,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - - - - + + + + @@ -84,13 +85,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + @@ -98,7 +99,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/DigestorMotif.xml b/tools/openms/DigestorMotif.xml index 4571b2afd..af1e314d4 100644 --- a/tools/openms/DigestorMotif.xml +++ b/tools/openms/DigestorMotif.xml @@ -38,12 +38,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - + + + + + + @@ -79,12 +79,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/EICExtractor.xml b/tools/openms/EICExtractor.xml index a69222e20..0f8dbd3d1 100644 --- a/tools/openms/EICExtractor.xml +++ b/tools/openms/EICExtractor.xml @@ -87,10 +87,10 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + @@ -102,24 +102,24 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - - - - + + + +
- - + +
- + - + diff --git a/tools/openms/ERPairFinder.xml b/tools/openms/ERPairFinder.xml index fea6b0729..e6a103a2a 100644 --- a/tools/openms/ERPairFinder.xml +++ b/tools/openms/ERPairFinder.xml @@ -55,17 +55,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - - - - - + + + + + - + diff --git a/tools/openms/Epifany.xml b/tools/openms/Epifany.xml index d77dd3f35..b667797b2 100644 --- a/tools/openms/Epifany.xml +++ b/tools/openms/Epifany.xml @@ -61,56 +61,57 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + + value != "select a value" - + - +
- - + +
- - - - + + + +
- + - - - - + + + +
- +
@@ -121,14 +122,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + diff --git a/tools/openms/ExternalCalibration.xml b/tools/openms/ExternalCalibration.xml index 69d79c719..837f3c421 100644 --- a/tools/openms/ExternalCalibration.xml +++ b/tools/openms/ExternalCalibration.xml @@ -38,16 +38,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - + + + + + - + diff --git a/tools/openms/FalseDiscoveryRate.xml b/tools/openms/FalseDiscoveryRate.xml index 011c89433..0d7b8804f 100644 --- a/tools/openms/FalseDiscoveryRate.xml +++ b/tools/openms/FalseDiscoveryRate.xml @@ -38,13 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - + +
@@ -62,7 +62,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/FeatureFinderCentroided.xml b/tools/openms/FeatureFinderCentroided.xml index e95f03911..ef79b5886 100644 --- a/tools/openms/FeatureFinderCentroided.xml +++ b/tools/openms/FeatureFinderCentroided.xml @@ -59,51 +59,51 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- +
- +
- - - - + + + +
- - - - - - - - - + + + + + + + + +
- +
- +
- - - - - - + + + + + + - - + + @@ -111,14 +111,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - + + +
- + diff --git a/tools/openms/FeatureFinderIdentification.xml b/tools/openms/FeatureFinderIdentification.xml index dd25422e3..7896f1fdb 100644 --- a/tools/openms/FeatureFinderIdentification.xml +++ b/tools/openms/FeatureFinderIdentification.xml @@ -105,80 +105,80 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + - +
- - - - - - + + + + + +
- - - - + + + +
- + - + - - + + - + - + - - + + - + - +
- + - +
- - - - + + + +
- +
- + diff --git a/tools/openms/FeatureFinderIsotopeWavelet.xml b/tools/openms/FeatureFinderIsotopeWavelet.xml index d3981cfa0..8e6c2e36c 100644 --- a/tools/openms/FeatureFinderIsotopeWavelet.xml +++ b/tools/openms/FeatureFinderIsotopeWavelet.xml @@ -38,11 +38,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + + @@ -51,13 +51,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - + +
- + diff --git a/tools/openms/FeatureFinderMRM.xml b/tools/openms/FeatureFinderMRM.xml index e72e102eb..51c92b3ce 100644 --- a/tools/openms/FeatureFinderMRM.xml +++ b/tools/openms/FeatureFinderMRM.xml @@ -38,18 +38,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + +
- + diff --git a/tools/openms/FeatureFinderMetabo.xml b/tools/openms/FeatureFinderMetabo.xml index c25c03c15..1b5ca1d4a 100644 --- a/tools/openms/FeatureFinderMetabo.xml +++ b/tools/openms/FeatureFinderMetabo.xml @@ -51,52 +51,52 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + +
- + - + - + - - - - + + + +
- + - - + +
- - - - + + + + - + @@ -108,14 +108,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + diff --git a/tools/openms/FeatureFinderMetaboIdent.xml b/tools/openms/FeatureFinderMetaboIdent.xml index 4d1aa3174..00ae0de81 100644 --- a/tools/openms/FeatureFinderMetaboIdent.xml +++ b/tools/openms/FeatureFinderMetaboIdent.xml @@ -85,44 +85,44 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- - - - + + + +
- - - + + +
- + - +
- - - - + + + +
- +
- + diff --git a/tools/openms/FeatureFinderMultiplex.xml b/tools/openms/FeatureFinderMultiplex.xml index 85ff41dd1..d87d5de5f 100644 --- a/tools/openms/FeatureFinderMultiplex.xml +++ b/tools/openms/FeatureFinderMultiplex.xml @@ -67,38 +67,38 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + - + - + - - - - - + + + + + - - - - - - + + + + + + - + @@ -107,24 +107,24 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - - - - - - - - - - - - + + + + + + + + + + + + + +
- + diff --git a/tools/openms/FeatureLinkerLabeled.xml b/tools/openms/FeatureLinkerLabeled.xml index a80e492d5..8355d8926 100644 --- a/tools/openms/FeatureLinkerLabeled.xml +++ b/tools/openms/FeatureLinkerLabeled.xml @@ -38,21 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - + + + + - +
- + diff --git a/tools/openms/FeatureLinkerUnlabeled.xml b/tools/openms/FeatureLinkerUnlabeled.xml index 87787d671..11429e890 100644 --- a/tools/openms/FeatureLinkerUnlabeled.xml +++ b/tools/openms/FeatureLinkerUnlabeled.xml @@ -61,38 +61,38 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - +
- +
- - - + + +
- - + + - - + +
- - - + + + @@ -101,7 +101,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + diff --git a/tools/openms/FeatureLinkerUnlabeledKD.xml b/tools/openms/FeatureLinkerUnlabeledKD.xml index 9eb31b4dd..f54bc5154 100644 --- a/tools/openms/FeatureLinkerUnlabeledKD.xml +++ b/tools/openms/FeatureLinkerUnlabeledKD.xml @@ -61,39 +61,39 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - +
- + - +
- - - - - + + + + +
- - - + + + - + @@ -101,33 +101,33 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- - + +
- - + +
- - - + + +
- - - - + + + + - + @@ -137,7 +137,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + diff --git a/tools/openms/FeatureLinkerUnlabeledQT.xml b/tools/openms/FeatureLinkerUnlabeledQT.xml index 24a3109f8..19ce0c7e2 100644 --- a/tools/openms/FeatureLinkerUnlabeledQT.xml +++ b/tools/openms/FeatureLinkerUnlabeledQT.xml @@ -61,41 +61,41 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - +
- - - - + + + +
- - - + + +
- - + + - - + +
- - - + + + @@ -104,7 +104,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + diff --git a/tools/openms/FileConverter.xml b/tools/openms/FileConverter.xml index 22371cf91..f8211cd47 100644 --- a/tools/openms/FileConverter.xml +++ b/tools/openms/FileConverter.xml @@ -38,8 +38,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -50,10 +50,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard + value != "select a value" - + @@ -64,7 +65,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -73,13 +74,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/FileFilter.xml b/tools/openms/FileFilter.xml index a69e0f829..21b6fa5b1 100644 --- a/tools/openms/FileFilter.xml +++ b/tools/openms/FileFilter.xml @@ -62,47 +62,48 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - + - + - +
- + - + - + - + - + @@ -110,22 +111,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - - + + - + @@ -174,10 +175,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -219,10 +220,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -231,22 +232,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - + + + +
- +
@@ -261,16 +262,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- + - + @@ -286,7 +287,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -299,26 +300,26 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- - - - - - - - + + + + + + + +
- + diff --git a/tools/openms/FileInfo.xml b/tools/openms/FileInfo.xml index a8eb96a4d..d742977dc 100644 --- a/tools/openms/FileInfo.xml +++ b/tools/openms/FileInfo.xml @@ -51,7 +51,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -61,7 +61,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/FileMerger.xml b/tools/openms/FileMerger.xml index aca65032a..19afa0063 100644 --- a/tools/openms/FileMerger.xml +++ b/tools/openms/FileMerger.xml @@ -67,13 +67,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + @@ -81,13 +81,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - +
- +
@@ -95,11 +95,11 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - +
- + diff --git a/tools/openms/FuzzyDiff.xml b/tools/openms/FuzzyDiff.xml index d686b4535..80ab4c28b 100644 --- a/tools/openms/FuzzyDiff.xml +++ b/tools/openms/FuzzyDiff.xml @@ -39,15 +39,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - - + + + + + + + - + @@ -56,7 +56,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/GNPSExport.xml b/tools/openms/GNPSExport.xml index 3a5771039..0e0ff93b7 100644 --- a/tools/openms/GNPSExport.xml +++ b/tools/openms/GNPSExport.xml @@ -78,32 +78,32 @@ ${' '.join(["'in_mzml_cond.in_mzml/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.elem - + - + - + - + - - + +
- +
- + diff --git a/tools/openms/HighResPrecursorMassCorrector.xml b/tools/openms/HighResPrecursorMassCorrector.xml index 4387a0cde..a3a05ebdd 100644 --- a/tools/openms/HighResPrecursorMassCorrector.xml +++ b/tools/openms/HighResPrecursorMassCorrector.xml @@ -59,32 +59,32 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - + + - - + +
- - + +
- - + + @@ -92,7 +92,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/IDConflictResolver.xml b/tools/openms/IDConflictResolver.xml index a51bf7ac9..4781b30db 100644 --- a/tools/openms/IDConflictResolver.xml +++ b/tools/openms/IDConflictResolver.xml @@ -38,15 +38,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + diff --git a/tools/openms/IDExtractor.xml b/tools/openms/IDExtractor.xml index 4e766bb1b..a43fb5cab 100644 --- a/tools/openms/IDExtractor.xml +++ b/tools/openms/IDExtractor.xml @@ -38,13 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - + diff --git a/tools/openms/IDFileConverter.xml b/tools/openms/IDFileConverter.xml index 809c4d44f..e34aa898e 100644 --- a/tools/openms/IDFileConverter.xml +++ b/tools/openms/IDFileConverter.xml @@ -46,8 +46,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -55,6 +55,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard + value != "select a value" @@ -62,21 +63,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + - - + + @@ -90,17 +91,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - - - - - - + + + + + + + + + + + @@ -136,10 +137,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - + + + +
@@ -148,11 +149,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - + diff --git a/tools/openms/IDFilter.xml b/tools/openms/IDFilter.xml index 95693f8fd..312b25589 100644 --- a/tools/openms/IDFilter.xml +++ b/tools/openms/IDFilter.xml @@ -78,30 +78,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + - + - + - +
- - - + + +
@@ -111,7 +111,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -3087,7 +3087,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6060,7 +6060,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + @@ -6096,20 +6096,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - +
- + - + @@ -6147,21 +6147,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - + +
- - + +
- - - + + + @@ -6169,9 +6169,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - +
@@ -6182,7 +6182,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/IDMapper.xml b/tools/openms/IDMapper.xml index e852065f1..4266acfa2 100644 --- a/tools/openms/IDMapper.xml +++ b/tools/openms/IDMapper.xml @@ -50,16 +50,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - + + + + + - + @@ -78,7 +78,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/IDMassAccuracy.xml b/tools/openms/IDMassAccuracy.xml index e5f69c378..2fbbf72ab 100644 --- a/tools/openms/IDMassAccuracy.xml +++ b/tools/openms/IDMassAccuracy.xml @@ -105,10 +105,10 @@ ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_ - + - + @@ -117,19 +117,19 @@ ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_ - + - + - + - + - + diff --git a/tools/openms/IDMerger.xml b/tools/openms/IDMerger.xml index 0f151ec78..8b9ad50f2 100644 --- a/tools/openms/IDMerger.xml +++ b/tools/openms/IDMerger.xml @@ -61,15 +61,16 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + + value != "select a value" @@ -78,7 +79,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + diff --git a/tools/openms/IDPosteriorErrorProbability.xml b/tools/openms/IDPosteriorErrorProbability.xml index 07dcdfcf8..16fcc2fca 100644 --- a/tools/openms/IDPosteriorErrorProbability.xml +++ b/tools/openms/IDPosteriorErrorProbability.xml @@ -51,21 +51,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - + + - - - + + + @@ -74,9 +74,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + diff --git a/tools/openms/IDRTCalibration.xml b/tools/openms/IDRTCalibration.xml index d92eb6040..6fd1a91d3 100644 --- a/tools/openms/IDRTCalibration.xml +++ b/tools/openms/IDRTCalibration.xml @@ -38,14 +38,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - + + + + + - + diff --git a/tools/openms/IDRipper.xml b/tools/openms/IDRipper.xml index 091bcd5f8..973aff849 100644 --- a/tools/openms/IDRipper.xml +++ b/tools/openms/IDRipper.xml @@ -37,12 +37,12 @@ out/ - + - + diff --git a/tools/openms/IDScoreSwitcher.xml b/tools/openms/IDScoreSwitcher.xml index 977c425e8..8e615ae63 100644 --- a/tools/openms/IDScoreSwitcher.xml +++ b/tools/openms/IDScoreSwitcher.xml @@ -38,7 +38,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -56,7 +56,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/IDSplitter.xml b/tools/openms/IDSplitter.xml index 67e35dee1..ac90092d5 100644 --- a/tools/openms/IDSplitter.xml +++ b/tools/openms/IDSplitter.xml @@ -57,10 +57,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/InternalCalibration.xml b/tools/openms/InternalCalibration.xml index 32f411b0e..7d92d6318 100644 --- a/tools/openms/InternalCalibration.xml +++ b/tools/openms/InternalCalibration.xml @@ -117,18 +117,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - +
- + @@ -138,17 +138,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - + + +
- - + +
- + diff --git a/tools/openms/IsobaricAnalyzer.xml b/tools/openms/IsobaricAnalyzer.xml index 7ba4e07ca..93d252df0 100644 --- a/tools/openms/IsobaricAnalyzer.xml +++ b/tools/openms/IsobaricAnalyzer.xml @@ -38,7 +38,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -48,9 +48,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + @@ -71,13 +71,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + - - + +
@@ -93,8 +93,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -124,8 +124,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -165,7 +165,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -178,7 +178,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -217,7 +217,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -231,7 +231,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -285,7 +285,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -304,7 +304,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -364,7 +364,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -385,7 +385,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -409,15 +409,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- + diff --git a/tools/openms/JSONExporter.xml b/tools/openms/JSONExporter.xml index 58d7fdb1d..7a0d35ad1 100644 --- a/tools/openms/JSONExporter.xml +++ b/tools/openms/JSONExporter.xml @@ -38,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/LuciphorAdapter.xml b/tools/openms/LuciphorAdapter.xml index eb2072b99..919fa4f38 100644 --- a/tools/openms/LuciphorAdapter.xml +++ b/tools/openms/LuciphorAdapter.xml @@ -42,21 +42,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - - + + - - + + @@ -3023,30 +3023,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - + + - - - - - - - + + + + + + + - + - + diff --git a/tools/openms/MRMMapper.xml b/tools/openms/MRMMapper.xml index e9fc38a47..f5f1d0a4e 100644 --- a/tools/openms/MRMMapper.xml +++ b/tools/openms/MRMMapper.xml @@ -42,17 +42,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- - + +
- + diff --git a/tools/openms/MRMPairFinder.xml b/tools/openms/MRMPairFinder.xml index 92b2549af..f42e179bb 100644 --- a/tools/openms/MRMPairFinder.xml +++ b/tools/openms/MRMPairFinder.xml @@ -55,14 +55,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - - + + + - + diff --git a/tools/openms/MRMTransitionGroupPicker.xml b/tools/openms/MRMTransitionGroupPicker.xml index 444d213ba..17e1546b6 100644 --- a/tools/openms/MRMTransitionGroupPicker.xml +++ b/tools/openms/MRMTransitionGroupPicker.xml @@ -42,18 +42,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- - - - + + + + - + @@ -62,29 +62,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - +
- - - + + + - - - - + + + + - + @@ -92,13 +92,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + @@ -110,7 +110,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/MSFraggerAdapter.xml b/tools/openms/MSFraggerAdapter.xml index e4bd4e8ec..29c8713b7 100644 --- a/tools/openms/MSFraggerAdapter.xml +++ b/tools/openms/MSFraggerAdapter.xml @@ -55,36 +55,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + + value != "select a value" - - - + + +
- - - + + + - - + + - - + + - + @@ -93,7 +94,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + @@ -129,19 +130,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - + - + @@ -150,10 +151,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - + + + +
@@ -170,7 +171,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -179,15 +180,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - - - + + + + + + @@ -195,45 +196,45 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- - - - - - - - - + + + + + + + + +
- - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + @@ -243,12 +244,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -257,18 +258,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - + +
- + @@ -305,7 +306,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -316,7 +317,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/MSGFPlusAdapter.xml b/tools/openms/MSGFPlusAdapter.xml index b7fbd0198..df450a0ff 100644 --- a/tools/openms/MSGFPlusAdapter.xml +++ b/tools/openms/MSGFPlusAdapter.xml @@ -69,32 +69,32 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - + + + + - + - + - + - + @@ -107,7 +107,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -116,22 +116,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - - - - + + + + + - - - - + + + + @@ -3098,7 +3098,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6071,12 +6071,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -6085,18 +6085,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - + +
- + @@ -6133,7 +6133,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6145,7 +6145,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/MSstatsConverter.xml b/tools/openms/MSstatsConverter.xml index 34d271102..55420878b 100644 --- a/tools/openms/MSstatsConverter.xml +++ b/tools/openms/MSstatsConverter.xml @@ -63,20 +63,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - + - + - + @@ -90,10 +90,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -102,7 +102,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/MapAlignerIdentification.xml b/tools/openms/MapAlignerIdentification.xml index a27cd9361..33cac9d1e 100644 --- a/tools/openms/MapAlignerIdentification.xml +++ b/tools/openms/MapAlignerIdentification.xml @@ -87,32 +87,32 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - +
- +
- - - + + +
- + @@ -121,48 +121,48 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + - - - - + + + +
- - - + + + - +
- - - - + + + + - + @@ -170,13 +170,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + @@ -186,7 +186,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + diff --git a/tools/openms/MapAlignerPoseClustering.xml b/tools/openms/MapAlignerPoseClustering.xml index 9a494506d..cfa5bf066 100644 --- a/tools/openms/MapAlignerPoseClustering.xml +++ b/tools/openms/MapAlignerPoseClustering.xml @@ -79,26 +79,26 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - +
- +
- +
- - - - - - - + + + + + + + @@ -107,29 +107,29 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- +
- - - + + +
- - + + - - + +
- - - + + + @@ -139,7 +139,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + diff --git a/tools/openms/MapAlignerSpectrum.xml b/tools/openms/MapAlignerSpectrum.xml index 339da48cc..1912c4c97 100644 --- a/tools/openms/MapAlignerSpectrum.xml +++ b/tools/openms/MapAlignerSpectrum.xml @@ -74,27 +74,27 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - +
- - - - - - - + + + + + + +
- + @@ -103,48 +103,48 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + - - - - + + + +
- - - + + + - +
- - - - + + + + - + @@ -152,13 +152,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + @@ -168,7 +168,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + diff --git a/tools/openms/MapAlignerTreeGuided.xml b/tools/openms/MapAlignerTreeGuided.xml index ea0884dfa..bca21011e 100644 --- a/tools/openms/MapAlignerTreeGuided.xml +++ b/tools/openms/MapAlignerTreeGuided.xml @@ -74,14 +74,14 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - +
- + @@ -89,7 +89,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + @@ -98,48 +98,48 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + - - - - + + + +
- - - + + + - +
- - - - + + + + - + @@ -147,13 +147,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + @@ -166,9 +166,9 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - - - + + + @@ -176,7 +176,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + diff --git a/tools/openms/MapNormalizer.xml b/tools/openms/MapNormalizer.xml index a06222b59..657d2e798 100644 --- a/tools/openms/MapNormalizer.xml +++ b/tools/openms/MapNormalizer.xml @@ -38,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/MapRTTransformer.xml b/tools/openms/MapRTTransformer.xml index a91f92427..85b0cdaca 100644 --- a/tools/openms/MapRTTransformer.xml +++ b/tools/openms/MapRTTransformer.xml @@ -66,11 +66,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + @@ -80,48 +80,48 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + - - - - + + + +
- - - + + + - +
- - - - + + + + - + @@ -129,13 +129,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + @@ -145,7 +145,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/MapStatistics.xml b/tools/openms/MapStatistics.xml index 6b9f73276..c401d3dd6 100644 --- a/tools/openms/MapStatistics.xml +++ b/tools/openms/MapStatistics.xml @@ -38,14 +38,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + diff --git a/tools/openms/MascotAdapter.xml b/tools/openms/MascotAdapter.xml index 372a78d82..67d36732a 100644 --- a/tools/openms/MascotAdapter.xml +++ b/tools/openms/MascotAdapter.xml @@ -38,18 +38,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - + - - - + + + @@ -125,17 +126,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - + - + @@ -157,27 +158,27 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - - - - - + + + + + + + + + + - + - + diff --git a/tools/openms/MascotAdapterOnline.xml b/tools/openms/MascotAdapterOnline.xml index b3a6881ec..2db59705d 100644 --- a/tools/openms/MascotAdapterOnline.xml +++ b/tools/openms/MascotAdapterOnline.xml @@ -38,45 +38,45 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + - + - + - + - - - + + + - - + + - + - + - + @@ -3043,7 +3043,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6010,21 +6010,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - + - + - + @@ -6035,19 +6035,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - + + - + @@ -6062,15 +6062,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - +
- + diff --git a/tools/openms/MassCalculator.xml b/tools/openms/MassCalculator.xml index 982216956..7e4f396fa 100644 --- a/tools/openms/MassCalculator.xml +++ b/tools/openms/MassCalculator.xml @@ -56,10 +56,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -67,7 +67,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -85,7 +85,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/MassTraceExtractor.xml b/tools/openms/MassTraceExtractor.xml index 145d57a19..92f956e3f 100644 --- a/tools/openms/MassTraceExtractor.xml +++ b/tools/openms/MassTraceExtractor.xml @@ -38,53 +38,54 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value"
- - - + + +
- + - + - + - - - - + + + +
- + - - + +
- + diff --git a/tools/openms/MetaProSIP.xml b/tools/openms/MetaProSIP.xml index 67e716b6f..d0bb51fdc 100644 --- a/tools/openms/MetaProSIP.xml +++ b/tools/openms/MetaProSIP.xml @@ -50,17 +50,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - - - - - - + + + + + + + + + + + @@ -69,7 +69,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -82,23 +82,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - - - - - + + + + + + + + + + - + - + diff --git a/tools/openms/MetaboliteSpectralMatcher.xml b/tools/openms/MetaboliteSpectralMatcher.xml index 2edbe0c17..6df40a19c 100644 --- a/tools/openms/MetaboliteSpectralMatcher.xml +++ b/tools/openms/MetaboliteSpectralMatcher.xml @@ -55,22 +55,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- - - + + + - + - + @@ -79,7 +79,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/MultiplexResolver.xml b/tools/openms/MultiplexResolver.xml index fa1d8283e..a3406fdc9 100644 --- a/tools/openms/MultiplexResolver.xml +++ b/tools/openms/MultiplexResolver.xml @@ -59,36 +59,36 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + - - - - + + + +
- - - - - - - - - - - - - - + + + + + + + + + + + + + +
- + diff --git a/tools/openms/MzMLSplitter.xml b/tools/openms/MzMLSplitter.xml index 7eb19fa36..77d12fff0 100644 --- a/tools/openms/MzMLSplitter.xml +++ b/tools/openms/MzMLSplitter.xml @@ -37,10 +37,10 @@ out/ - - - - + + + + @@ -50,7 +50,7 @@ out/ - + diff --git a/tools/openms/MzTabExporter.xml b/tools/openms/MzTabExporter.xml index 5711258e1..34c22f633 100644 --- a/tools/openms/MzTabExporter.xml +++ b/tools/openms/MzTabExporter.xml @@ -43,7 +43,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -51,7 +51,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/NoiseFilterGaussian.xml b/tools/openms/NoiseFilterGaussian.xml index c6c198886..0b412f7f0 100644 --- a/tools/openms/NoiseFilterGaussian.xml +++ b/tools/openms/NoiseFilterGaussian.xml @@ -38,21 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - + +
- + - + diff --git a/tools/openms/NoiseFilterSGolay.xml b/tools/openms/NoiseFilterSGolay.xml index 166394973..d7817a49b 100644 --- a/tools/openms/NoiseFilterSGolay.xml +++ b/tools/openms/NoiseFilterSGolay.xml @@ -38,19 +38,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - + +
- + - + diff --git a/tools/openms/NovorAdapter.xml b/tools/openms/NovorAdapter.xml index 4e6ade2d6..a296b9cea 100644 --- a/tools/openms/NovorAdapter.xml +++ b/tools/openms/NovorAdapter.xml @@ -46,30 +46,30 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + - + - - - + + + - + @@ -98,7 +98,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -127,7 +127,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -135,7 +135,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/NucleicAcidSearchEngine.xml b/tools/openms/NucleicAcidSearchEngine.xml index bf1c0c00f..31821754e 100644 --- a/tools/openms/NucleicAcidSearchEngine.xml +++ b/tools/openms/NucleicAcidSearchEngine.xml @@ -117,37 +117,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - + + - - + + - + - +
- - + + - + @@ -161,7 +161,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + @@ -535,14 +535,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - + + + + @@ -557,19 +557,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- +
- +
- + diff --git a/tools/openms/OpenMSDatabasesInfo.xml b/tools/openms/OpenMSDatabasesInfo.xml index b1e194f03..a451fc817 100644 --- a/tools/openms/OpenMSDatabasesInfo.xml +++ b/tools/openms/OpenMSDatabasesInfo.xml @@ -40,7 +40,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/OpenMSInfo.xml b/tools/openms/OpenMSInfo.xml index 1dbcbb54b..81238dd1c 100644 --- a/tools/openms/OpenMSInfo.xml +++ b/tools/openms/OpenMSInfo.xml @@ -47,7 +47,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/OpenPepXL.xml b/tools/openms/OpenPepXL.xml index ffb233475..98653cd93 100644 --- a/tools/openms/OpenPepXL.xml +++ b/tools/openms/OpenPepXL.xml @@ -97,37 +97,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - + + + +
- - + + - - - + + +
- - - + + +
- + @@ -3094,7 +3094,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6061,12 +6061,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + + @@ -6104,26 +6104,26 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + - - - + + + - +
- - + + @@ -6142,7 +6142,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/OpenPepXLLF.xml b/tools/openms/OpenPepXLLF.xml index 285ef9998..e95e091b0 100644 --- a/tools/openms/OpenPepXLLF.xml +++ b/tools/openms/OpenPepXLLF.xml @@ -93,36 +93,36 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + +
- - + + - - - + + +
- - - + + +
- + @@ -3089,7 +3089,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6056,12 +6056,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + + @@ -6099,32 +6099,32 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + - - + + - +
- - + + - +
@@ -6138,7 +6138,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/OpenSwathAnalyzer.xml b/tools/openms/OpenSwathAnalyzer.xml index 17729663e..bf4b87beb 100644 --- a/tools/openms/OpenSwathAnalyzer.xml +++ b/tools/openms/OpenSwathAnalyzer.xml @@ -67,8 +67,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -80,12 +80,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - +
- + @@ -95,37 +95,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - - + + + + - + - - - - - + + + + + - +
- - - - + + + + - + @@ -134,29 +134,29 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - +
- - - + + + - - - - + + + + - + @@ -164,13 +164,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + @@ -181,27 +181,27 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - + + - - - - - + + + + +
- - - + + +
- - + +
@@ -229,7 +229,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/OpenSwathAssayGenerator.xml b/tools/openms/OpenSwathAssayGenerator.xml index 1ebae847d..e6a312699 100644 --- a/tools/openms/OpenSwathAssayGenerator.xml +++ b/tools/openms/OpenSwathAssayGenerator.xml @@ -54,40 +54,41 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - - - + + + - + - - - - - - + + + + + + - + - + diff --git a/tools/openms/OpenSwathChromatogramExtractor.xml b/tools/openms/OpenSwathChromatogramExtractor.xml index 3c39b4890..be2cb249f 100644 --- a/tools/openms/OpenSwathChromatogramExtractor.xml +++ b/tools/openms/OpenSwathChromatogramExtractor.xml @@ -65,23 +65,23 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + - - - - + + + +
- + @@ -91,13 +91,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + diff --git a/tools/openms/OpenSwathConfidenceScoring.xml b/tools/openms/OpenSwathConfidenceScoring.xml index e9151b5d4..5610f3585 100644 --- a/tools/openms/OpenSwathConfidenceScoring.xml +++ b/tools/openms/OpenSwathConfidenceScoring.xml @@ -50,19 +50,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - + +
- - - + + +
- + diff --git a/tools/openms/OpenSwathDIAPreScoring.xml b/tools/openms/OpenSwathDIAPreScoring.xml index b92aad1fe..41a7edcd9 100644 --- a/tools/openms/OpenSwathDIAPreScoring.xml +++ b/tools/openms/OpenSwathDIAPreScoring.xml @@ -52,23 +52,23 @@ ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(gext)s' 'output_files/%(bn)s - + - + - + - + - + diff --git a/tools/openms/OpenSwathDecoyGenerator.xml b/tools/openms/OpenSwathDecoyGenerator.xml index 42a340640..5d832dbc8 100644 --- a/tools/openms/OpenSwathDecoyGenerator.xml +++ b/tools/openms/OpenSwathDecoyGenerator.xml @@ -38,43 +38,44 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - + - + - - - - - - - - + + + + + + + + - + - + diff --git a/tools/openms/OpenSwathFeatureXMLToTSV.xml b/tools/openms/OpenSwathFeatureXMLToTSV.xml index d45d15296..d64c0da10 100644 --- a/tools/openms/OpenSwathFeatureXMLToTSV.xml +++ b/tools/openms/OpenSwathFeatureXMLToTSV.xml @@ -57,20 +57,20 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + - + diff --git a/tools/openms/OpenSwathFileSplitter.xml b/tools/openms/OpenSwathFileSplitter.xml index eabd79642..2853b400f 100644 --- a/tools/openms/OpenSwathFileSplitter.xml +++ b/tools/openms/OpenSwathFileSplitter.xml @@ -50,10 +50,10 @@ outputDirectory/ - + - + diff --git a/tools/openms/OpenSwathMzMLFileCacher.xml b/tools/openms/OpenSwathMzMLFileCacher.xml index 284e13084..39aeecfcb 100644 --- a/tools/openms/OpenSwathMzMLFileCacher.xml +++ b/tools/openms/OpenSwathMzMLFileCacher.xml @@ -38,20 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - + - + - + diff --git a/tools/openms/OpenSwathRTNormalizer.xml b/tools/openms/OpenSwathRTNormalizer.xml index 3674b432d..dbbd40d74 100644 --- a/tools/openms/OpenSwathRTNormalizer.xml +++ b/tools/openms/OpenSwathRTNormalizer.xml @@ -65,19 +65,19 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + - - + +
- + @@ -85,42 +85,42 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - - - + + +
- - - - + + + + - + - - - - - + + + + + - +
- - - - + + + + - + @@ -129,29 +129,29 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - - - + + + - +
- - - + + + - - - - + + + + - + @@ -159,13 +159,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- + - + @@ -176,27 +176,27 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- - + + - - - - - + + + + +
- - - + + +
- - + +
@@ -223,15 +223,15 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- - - - - + + + + +
- + diff --git a/tools/openms/OpenSwathRewriteToFeatureXML.xml b/tools/openms/OpenSwathRewriteToFeatureXML.xml index 2c687454d..7e71ad5f6 100644 --- a/tools/openms/OpenSwathRewriteToFeatureXML.xml +++ b/tools/openms/OpenSwathRewriteToFeatureXML.xml @@ -47,11 +47,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + diff --git a/tools/openms/OpenSwathWorkflow.xml b/tools/openms/OpenSwathWorkflow.xml index 6ad283b02..693748ae3 100644 --- a/tools/openms/OpenSwathWorkflow.xml +++ b/tools/openms/OpenSwathWorkflow.xml @@ -147,21 +147,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - - - - + + + + +
- + @@ -174,7 +174,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + @@ -184,14 +184,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + @@ -199,52 +199,52 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - - - - - + + + + +
- +
- +
- - - + + + - + - - - - - + + + + + - +
- - - + + + - + @@ -253,27 +253,27 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - +
- - - + + + - - + + - + @@ -281,13 +281,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - + @@ -298,21 +298,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - + + - - - - - + + + + +
- +
@@ -342,43 +342,43 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - - + + + - + - - + + - - - + + + - + - + @@ -389,15 +389,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - + + - + diff --git a/tools/openms/PSMFeatureExtractor.xml b/tools/openms/PSMFeatureExtractor.xml index 8171bec4b..b0c7e9126 100644 --- a/tools/openms/PSMFeatureExtractor.xml +++ b/tools/openms/PSMFeatureExtractor.xml @@ -53,15 +53,16 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + + value != "select a value" @@ -75,7 +76,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + diff --git a/tools/openms/PeakPickerHiRes.xml b/tools/openms/PeakPickerHiRes.xml index d8e006f41..4aeba9a0d 100644 --- a/tools/openms/PeakPickerHiRes.xml +++ b/tools/openms/PeakPickerHiRes.xml @@ -38,12 +38,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - + + + + - +
- - - - - - - - + + + + + + + +
- + - + diff --git a/tools/openms/PeakPickerIterative.xml b/tools/openms/PeakPickerIterative.xml index 1011bcc79..7a25f3302 100644 --- a/tools/openms/PeakPickerIterative.xml +++ b/tools/openms/PeakPickerIterative.xml @@ -38,21 +38,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - - - + + + + + +
- + diff --git a/tools/openms/PeakPickerWavelet.xml b/tools/openms/PeakPickerWavelet.xml index 2b8b5b412..17d5204f0 100644 --- a/tools/openms/PeakPickerWavelet.xml +++ b/tools/openms/PeakPickerWavelet.xml @@ -38,72 +38,72 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + + - - + +
- +
- - - - + + + +
- - + +
- - - - - + + + + +
- +
- - - - + + + +
- - - - + + + +
- - - - + + + +
- - - - - - - - - + + + + + + + + +
- + diff --git a/tools/openms/PeptideIndexer.xml b/tools/openms/PeptideIndexer.xml index ca16c2749..fd70bb1da 100644 --- a/tools/openms/PeptideIndexer.xml +++ b/tools/openms/PeptideIndexer.xml @@ -46,17 +46,17 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - + @@ -65,18 +65,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - + +
- + @@ -113,7 +113,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -123,7 +123,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/PercolatorAdapter.xml b/tools/openms/PercolatorAdapter.xml index e8c338cbd..53128d1ea 100644 --- a/tools/openms/PercolatorAdapter.xml +++ b/tools/openms/PercolatorAdapter.xml @@ -168,7 +168,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -180,17 +180,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + + value != "select a value" - + @@ -208,13 +209,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -222,37 +223,37 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - - - + + + + + + + - + - - + + - + - - - + + + - + diff --git a/tools/openms/PhosphoScoring.xml b/tools/openms/PhosphoScoring.xml index 4905ef3e7..438eb5a43 100644 --- a/tools/openms/PhosphoScoring.xml +++ b/tools/openms/PhosphoScoring.xml @@ -42,20 +42,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - + + + + - - - + + + - + diff --git a/tools/openms/PrecursorMassCorrector.xml b/tools/openms/PrecursorMassCorrector.xml index 984dc528e..4458c01be 100644 --- a/tools/openms/PrecursorMassCorrector.xml +++ b/tools/openms/PrecursorMassCorrector.xml @@ -46,14 +46,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - - + + - + diff --git a/tools/openms/ProteinInference.xml b/tools/openms/ProteinInference.xml index fc31198ec..eb016a50c 100644 --- a/tools/openms/ProteinInference.xml +++ b/tools/openms/ProteinInference.xml @@ -53,18 +53,19 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - + + value != "select a value" - + @@ -75,8 +76,8 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- - + + @@ -96,13 +97,13 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + diff --git a/tools/openms/ProteinQuantifier.xml b/tools/openms/ProteinQuantifier.xml index a7373ac77..38c7ea210 100644 --- a/tools/openms/ProteinQuantifier.xml +++ b/tools/openms/ProteinQuantifier.xml @@ -83,10 +83,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -96,8 +96,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - + + @@ -114,19 +114,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - +
- + diff --git a/tools/openms/ProteinResolver.xml b/tools/openms/ProteinResolver.xml index f0299cb87..7143a6c40 100644 --- a/tools/openms/ProteinResolver.xml +++ b/tools/openms/ProteinResolver.xml @@ -102,7 +102,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -112,7 +112,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -120,21 +120,21 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - + + +
- + - + - + @@ -144,7 +144,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/QCCalculator.xml b/tools/openms/QCCalculator.xml index 1413916cf..593b0c72b 100644 --- a/tools/openms/QCCalculator.xml +++ b/tools/openms/QCCalculator.xml @@ -62,13 +62,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - + @@ -86,7 +87,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/QCEmbedder.xml b/tools/openms/QCEmbedder.xml index 7d03792e8..6be1fb1d9 100644 --- a/tools/openms/QCEmbedder.xml +++ b/tools/openms/QCEmbedder.xml @@ -70,7 +70,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -81,7 +81,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/QCExporter.xml b/tools/openms/QCExporter.xml index a7e79b82c..6f8bd2953 100644 --- a/tools/openms/QCExporter.xml +++ b/tools/openms/QCExporter.xml @@ -42,15 +42,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - + diff --git a/tools/openms/QCExtractor.xml b/tools/openms/QCExtractor.xml index fee26e75a..65314c34e 100644 --- a/tools/openms/QCExtractor.xml +++ b/tools/openms/QCExtractor.xml @@ -46,8 +46,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -56,7 +56,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/QCImporter.xml b/tools/openms/QCImporter.xml index 219ea7a9a..4d25581cd 100644 --- a/tools/openms/QCImporter.xml +++ b/tools/openms/QCImporter.xml @@ -51,11 +51,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + diff --git a/tools/openms/QCMerger.xml b/tools/openms/QCMerger.xml index c2d937ee7..02c5e6157 100644 --- a/tools/openms/QCMerger.xml +++ b/tools/openms/QCMerger.xml @@ -53,10 +53,10 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + @@ -64,7 +64,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + diff --git a/tools/openms/QCShrinker.xml b/tools/openms/QCShrinker.xml index 979ef40f5..e75b2a3e8 100644 --- a/tools/openms/QCShrinker.xml +++ b/tools/openms/QCShrinker.xml @@ -46,7 +46,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -57,7 +57,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/QualityControl.xml b/tools/openms/QualityControl.xml index 83519f423..ee06ba0c5 100644 --- a/tools/openms/QualityControl.xml +++ b/tools/openms/QualityControl.xml @@ -135,7 +135,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -145,7 +145,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -157,7 +157,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -171,7 +171,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -181,20 +181,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + - +
- + diff --git a/tools/openms/RNADigestor.xml b/tools/openms/RNADigestor.xml index b5c3b971c..244473307 100644 --- a/tools/openms/RNADigestor.xml +++ b/tools/openms/RNADigestor.xml @@ -38,11 +38,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - + + + + + @@ -59,7 +59,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/RNAMassCalculator.xml b/tools/openms/RNAMassCalculator.xml index 53876282b..1abb63d5d 100644 --- a/tools/openms/RNAMassCalculator.xml +++ b/tools/openms/RNAMassCalculator.xml @@ -56,10 +56,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + @@ -68,7 +68,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -89,7 +89,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/RNPxlSearch.xml b/tools/openms/RNPxlSearch.xml index 6de417793..7ee3467f1 100644 --- a/tools/openms/RNPxlSearch.xml +++ b/tools/openms/RNPxlSearch.xml @@ -55,31 +55,31 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- - + + - - - + + +
- - + +
- + @@ -3046,7 +3046,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6013,13 +6013,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - + + + + @@ -6057,14 +6057,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- +
- + - + @@ -6072,22 +6072,22 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - + - + - + @@ -6097,12 +6097,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- + diff --git a/tools/openms/RNPxlXICFilter.xml b/tools/openms/RNPxlXICFilter.xml index 7b0c5f679..6805ab786 100644 --- a/tools/openms/RNPxlXICFilter.xml +++ b/tools/openms/RNPxlXICFilter.xml @@ -42,14 +42,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - - + + + + + - + diff --git a/tools/openms/SageAdapter.xml b/tools/openms/SageAdapter.xml index ca7e71ed1..a86b083c1 100644 --- a/tools/openms/SageAdapter.xml +++ b/tools/openms/SageAdapter.xml @@ -57,32 +57,32 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + - - + + - - - - + + + + - - - + + + - + @@ -118,7 +118,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + @@ -3085,7 +3085,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + @@ -6057,12 +6057,12 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - + @@ -6071,18 +6071,18 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + - - + +
- + @@ -6119,7 +6119,7 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi - + @@ -6129,28 +6129,28 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
- - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - + - + diff --git a/tools/openms/SeedListGenerator.xml b/tools/openms/SeedListGenerator.xml index afffca1fa..18b2b75c6 100644 --- a/tools/openms/SeedListGenerator.xml +++ b/tools/openms/SeedListGenerator.xml @@ -37,11 +37,11 @@ out_prefix/ - + - + diff --git a/tools/openms/SemanticValidator.xml b/tools/openms/SemanticValidator.xml index 91939a3d4..e267f1264 100644 --- a/tools/openms/SemanticValidator.xml +++ b/tools/openms/SemanticValidator.xml @@ -56,8 +56,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -67,12 +67,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/SequenceCoverageCalculator.xml b/tools/openms/SequenceCoverageCalculator.xml index 3f1ea939d..128481cbc 100644 --- a/tools/openms/SequenceCoverageCalculator.xml +++ b/tools/openms/SequenceCoverageCalculator.xml @@ -42,11 +42,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + diff --git a/tools/openms/SimpleSearchEngine.xml b/tools/openms/SimpleSearchEngine.xml index b4b9fa0eb..5c73d5bbd 100644 --- a/tools/openms/SimpleSearchEngine.xml +++ b/tools/openms/SimpleSearchEngine.xml @@ -42,10 +42,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + +
- + @@ -83,28 +83,28 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - + + - - - + + +
- - + +
- + @@ -3071,7 +3071,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6038,10 +6038,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + @@ -6051,20 +6051,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - + + +
- +
- + diff --git a/tools/openms/SiriusAdapter.xml b/tools/openms/SiriusAdapter.xml index 2bf81a8c5..73becd038 100644 --- a/tools/openms/SiriusAdapter.xml +++ b/tools/openms/SiriusAdapter.xml @@ -85,7 +85,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -97,20 +97,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - + + + - - + +
- + @@ -118,12 +118,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - - - + + + + - + @@ -136,23 +136,23 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + - + - + - + - +
@@ -165,7 +165,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/SpecLibCreator.xml b/tools/openms/SpecLibCreator.xml index 2e54224ca..16c1e8b18 100644 --- a/tools/openms/SpecLibCreator.xml +++ b/tools/openms/SpecLibCreator.xml @@ -42,15 +42,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - + - + diff --git a/tools/openms/SpecLibSearcher.xml b/tools/openms/SpecLibSearcher.xml index cd237eded..cf000859f 100644 --- a/tools/openms/SpecLibSearcher.xml +++ b/tools/openms/SpecLibSearcher.xml @@ -58,14 +58,14 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i - + - + - - + + @@ -75,32 +75,32 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i
- - + + - - - + + +
- +
- +
- - - - + + + +
- + @@ -3067,7 +3067,7 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i - + @@ -6034,11 +6034,11 @@ ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i - +
- + diff --git a/tools/openms/SpectraFilterBernNorm.xml b/tools/openms/SpectraFilterBernNorm.xml index dea23e2c3..690465db0 100644 --- a/tools/openms/SpectraFilterBernNorm.xml +++ b/tools/openms/SpectraFilterBernNorm.xml @@ -38,15 +38,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + +
- + diff --git a/tools/openms/SpectraFilterMarkerMower.xml b/tools/openms/SpectraFilterMarkerMower.xml index 245b2dda0..3cb371ac7 100644 --- a/tools/openms/SpectraFilterMarkerMower.xml +++ b/tools/openms/SpectraFilterMarkerMower.xml @@ -38,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/SpectraFilterNLargest.xml b/tools/openms/SpectraFilterNLargest.xml index e344604d4..61989a7c5 100644 --- a/tools/openms/SpectraFilterNLargest.xml +++ b/tools/openms/SpectraFilterNLargest.xml @@ -38,13 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- +
- + diff --git a/tools/openms/SpectraFilterNormalizer.xml b/tools/openms/SpectraFilterNormalizer.xml index d59186bce..38607665b 100644 --- a/tools/openms/SpectraFilterNormalizer.xml +++ b/tools/openms/SpectraFilterNormalizer.xml @@ -38,9 +38,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- + @@ -48,7 +48,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/SpectraFilterParentPeakMower.xml b/tools/openms/SpectraFilterParentPeakMower.xml index 4b8dec0f7..eceec7e10 100644 --- a/tools/openms/SpectraFilterParentPeakMower.xml +++ b/tools/openms/SpectraFilterParentPeakMower.xml @@ -38,20 +38,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - - - - - - + + + + + + + +
- + diff --git a/tools/openms/SpectraFilterScaler.xml b/tools/openms/SpectraFilterScaler.xml index 832843831..b6081b1b4 100644 --- a/tools/openms/SpectraFilterScaler.xml +++ b/tools/openms/SpectraFilterScaler.xml @@ -38,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/SpectraFilterSqrtMower.xml b/tools/openms/SpectraFilterSqrtMower.xml index 0b6112da1..425071b9e 100644 --- a/tools/openms/SpectraFilterSqrtMower.xml +++ b/tools/openms/SpectraFilterSqrtMower.xml @@ -38,10 +38,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/SpectraFilterThresholdMower.xml b/tools/openms/SpectraFilterThresholdMower.xml index b26c465b5..d40a04c27 100644 --- a/tools/openms/SpectraFilterThresholdMower.xml +++ b/tools/openms/SpectraFilterThresholdMower.xml @@ -38,13 +38,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- +
- + diff --git a/tools/openms/SpectraFilterWindowMower.xml b/tools/openms/SpectraFilterWindowMower.xml index 754e5c6fd..0d6f30913 100644 --- a/tools/openms/SpectraFilterWindowMower.xml +++ b/tools/openms/SpectraFilterWindowMower.xml @@ -38,11 +38,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - +
- - - + + + @@ -50,7 +50,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/SpectraMerger.xml b/tools/openms/SpectraMerger.xml index a80b670fd..d22051bc5 100644 --- a/tools/openms/SpectraMerger.xml +++ b/tools/openms/SpectraMerger.xml @@ -38,8 +38,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -47,64 +47,64 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- - + + - +
- + - - - - - + + + + +
- + - - - + + +
- + - - + +
- - - + + +
- + diff --git a/tools/openms/SpectraSTSearchAdapter.xml b/tools/openms/SpectraSTSearchAdapter.xml index 5a1eb6cf2..456d72660 100644 --- a/tools/openms/SpectraSTSearchAdapter.xml +++ b/tools/openms/SpectraSTSearchAdapter.xml @@ -86,34 +86,34 @@ ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn - + - + - + - + - + - + - + diff --git a/tools/openms/StaticModification.xml b/tools/openms/StaticModification.xml index 02833d7be..f9582dc97 100644 --- a/tools/openms/StaticModification.xml +++ b/tools/openms/StaticModification.xml @@ -38,8 +38,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -3006,14 +3006,14 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/TICCalculator.xml b/tools/openms/TICCalculator.xml index feaca4d6d..1b6f31ace 100644 --- a/tools/openms/TICCalculator.xml +++ b/tools/openms/TICCalculator.xml @@ -35,8 +35,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -48,7 +48,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/TOFCalibration.xml b/tools/openms/TOFCalibration.xml index de1f3d791..f41d1e153 100644 --- a/tools/openms/TOFCalibration.xml +++ b/tools/openms/TOFCalibration.xml @@ -50,77 +50,77 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - - + + + +
- - - + + + - - + +
- +
- - - - + + + +
- - + +
- - - - - + + + + +
- +
- - - - + + + +
- - - - + + + +
- - - - + + + +
- - - - - - - - - + + + + + + + + +
- + diff --git a/tools/openms/TargetedFileConverter.xml b/tools/openms/TargetedFileConverter.xml index dfc8508f6..e02942365 100644 --- a/tools/openms/TargetedFileConverter.xml +++ b/tools/openms/TargetedFileConverter.xml @@ -38,15 +38,16 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value"
- + @@ -58,7 +59,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + diff --git a/tools/openms/TextExporter.xml b/tools/openms/TextExporter.xml index 1596c0c5e..8869300be 100644 --- a/tools/openms/TextExporter.xml +++ b/tools/openms/TextExporter.xml @@ -71,17 +71,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + + value != "select a value" - + - + @@ -90,19 +91,19 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- +
- - - + + +
- + @@ -118,7 +119,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- + diff --git a/tools/openms/TriqlerConverter.xml b/tools/openms/TriqlerConverter.xml index 7955889b9..ed28e1cc3 100644 --- a/tools/openms/TriqlerConverter.xml +++ b/tools/openms/TriqlerConverter.xml @@ -63,9 +63,9 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - - + + + @@ -78,11 +78,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/XFDR.xml b/tools/openms/XFDR.xml index ec7b7e59d..a04816401 100644 --- a/tools/openms/XFDR.xml +++ b/tools/openms/XFDR.xml @@ -72,20 +72,20 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - - - + + + + - - + + - + diff --git a/tools/openms/XMLValidator.xml b/tools/openms/XMLValidator.xml index 9031f9fe3..2a398bde9 100644 --- a/tools/openms/XMLValidator.xml +++ b/tools/openms/XMLValidator.xml @@ -43,11 +43,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + diff --git a/tools/openms/XTandemAdapter.xml b/tools/openms/XTandemAdapter.xml index bd1ee019d..ad112e6cb 100644 --- a/tools/openms/XTandemAdapter.xml +++ b/tools/openms/XTandemAdapter.xml @@ -69,25 +69,25 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + - - - + + + - + - + - + @@ -3054,7 +3054,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6021,8 +6021,8 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - - + + @@ -6049,26 +6049,26 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - + - +
- + - + @@ -6077,18 +6077,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + - - + +
- + @@ -6125,7 +6125,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard - + @@ -6136,7 +6136,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
- +