From b4071d77aa10a547a845cdffce8fcc63c1b37d00 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 6 Feb 2021 15:11:54 +0100
Subject: [PATCH] OpenMS place each in/output synlink in unique dir

before each symlink was placed in a dir named by the name of the
corresponding parameter. this still allows for conflicts if several
data sets have the sem identifier.

solution: place symlinks in directory parameter_name/galaxy-dataset-id

usecase: ConsensusID takes the result of different search engines
for the same sample. then the identifiers of the inputs are all the
sample name which leads to a conflict.
---
 tools/openms/404-urls.patch                   |  2 +-
 tools/openms/AccurateMassSearch.xml           | 11 +++++---
 tools/openms/AssayGeneratorMetabo.xml         | 13 +++++----
 tools/openms/BaselineFilter.xml               |  1 +
 tools/openms/CVInspector.xml                  |  6 +++--
 tools/openms/ClusterMassTraces.xml            |  1 +
 tools/openms/ClusterMassTracesByPrecursor.xml |  1 +
 tools/openms/CometAdapter.xml                 |  1 +
 tools/openms/CompNovo.xml                     |  1 +
 tools/openms/CompNovoCID.xml                  |  1 +
 tools/openms/ConsensusID.xml                  |  6 +++--
 tools/openms/ConsensusMapNormalizer.xml       |  1 +
 tools/openms/CruxAdapter.xml                  |  1 +
 tools/openms/DTAExtractor.xml                 |  1 +
 tools/openms/DatabaseFilter.xml               |  1 +
 tools/openms/DatabaseSuitability.xml          |  1 +
 tools/openms/DeMeanderize.xml                 |  1 +
 tools/openms/Decharger.xml                    |  1 +
 tools/openms/DecoyDatabase.xml                |  6 +++--
 tools/openms/Digestor.xml                     |  1 +
 tools/openms/DigestorMotif.xml                |  1 +
 tools/openms/EICExtractor.xml                 | 11 +++++---
 tools/openms/ERPairFinder.xml                 |  1 +
 tools/openms/Epifany.xml                      |  6 +++--
 tools/openms/ExternalCalibration.xml          |  1 +
 tools/openms/FFEval.xml                       |  1 +
 tools/openms/FalseDiscoveryRate.xml           |  1 +
 tools/openms/FeatureFinderCentroided.xml      |  1 +
 tools/openms/FeatureFinderIdentification.xml  |  1 +
 tools/openms/FeatureFinderIsotopeWavelet.xml  |  1 +
 tools/openms/FeatureFinderMRM.xml             |  1 +
 tools/openms/FeatureFinderMetabo.xml          |  1 +
 tools/openms/FeatureFinderMetaboIdent.xml     |  1 +
 tools/openms/FeatureFinderMultiplex.xml       |  1 +
 tools/openms/FeatureFinderSuperHirn.xml       |  1 +
 tools/openms/FeatureLinkerLabeled.xml         |  1 +
 tools/openms/FeatureLinkerUnlabeled.xml       |  6 +++--
 tools/openms/FeatureLinkerUnlabeledKD.xml     |  6 +++--
 tools/openms/FeatureLinkerUnlabeledQT.xml     |  6 +++--
 tools/openms/FidoAdapter.xml                  |  1 +
 tools/openms/FileConverter.xml                |  1 +
 tools/openms/FileFilter.xml                   |  1 +
 tools/openms/FileInfo.xml                     |  1 +
 tools/openms/FileMerger.xml                   | 13 +++++----
 tools/openms/FuzzyDiff.xml                    |  1 +
 tools/openms/GNPSExport.xml                   |  6 +++--
 .../openms/HighResPrecursorMassCorrector.xml  |  1 +
 tools/openms/IDConflictResolver.xml           |  1 +
 tools/openms/IDExtractor.xml                  |  1 +
 tools/openms/IDFileConverter.xml              |  1 +
 tools/openms/IDFilter.xml                     |  1 +
 tools/openms/IDMapper.xml                     |  1 +
 tools/openms/IDMassAccuracy.xml               | 11 +++++---
 tools/openms/IDMerger.xml                     |  6 +++--
 tools/openms/IDPosteriorErrorProbability.xml  |  1 +
 tools/openms/IDRTCalibration.xml              |  1 +
 tools/openms/IDRipper.xml                     |  3 ++-
 tools/openms/IDScoreSwitcher.xml              |  1 +
 tools/openms/IDSplitter.xml                   |  1 +
 tools/openms/InternalCalibration.xml          |  1 +
 tools/openms/IsobaricAnalyzer.xml             |  1 +
 tools/openms/LabeledEval.xml                  |  1 +
 tools/openms/LuciphorAdapter.xml              |  3 ++-
 tools/openms/MRMMapper.xml                    |  1 +
 tools/openms/MRMPairFinder.xml                |  1 +
 tools/openms/MRMTransitionGroupPicker.xml     |  1 +
 tools/openms/MSFraggerAdapter.xml             |  3 ++-
 tools/openms/MSGFPlusAdapter.xml              |  3 ++-
 tools/openms/MSSimulator.xml                  |  6 +++--
 tools/openms/MSstatsConverter.xml             |  6 +++--
 tools/openms/MaRaClusterAdapter.xml           | 11 +++++---
 tools/openms/MapAlignerIdentification.xml     | 18 ++++++++-----
 tools/openms/MapAlignerPoseClustering.xml     | 18 ++++++++-----
 tools/openms/MapAlignerSpectrum.xml           | 20 ++++++++------
 tools/openms/MapAlignerTreeGuided.xml         | 20 ++++++++------
 tools/openms/MapNormalizer.xml                |  1 +
 tools/openms/MapRTTransformer.xml             |  1 +
 tools/openms/MapStatistics.xml                |  1 +
 tools/openms/MascotAdapter.xml                |  1 +
 tools/openms/MascotAdapterOnline.xml          |  1 +
 tools/openms/MassCalculator.xml               |  1 +
 tools/openms/MassTraceExtractor.xml           |  1 +
 tools/openms/MetaProSIP.xml                   |  1 +
 tools/openms/MetaboliteAdductDecharger.xml    |  1 +
 tools/openms/MetaboliteSpectralMatcher.xml    |  1 +
 tools/openms/MultiplexResolver.xml            |  1 +
 tools/openms/MyriMatchAdapter.xml             |  1 +
 tools/openms/MzMLSplitter.xml                 |  3 ++-
 tools/openms/MzTabExporter.xml                |  1 +
 tools/openms/NoiseFilterGaussian.xml          |  1 +
 tools/openms/NoiseFilterSGolay.xml            |  1 +
 tools/openms/NovorAdapter.xml                 |  3 ++-
 tools/openms/NucleicAcidSearchEngine.xml      |  1 +
 tools/openms/OMSSAAdapter.patch               |  2 +-
 tools/openms/OMSSAAdapter.xml                 |  1 +
 tools/openms/OpenPepXL.xml                    |  1 +
 tools/openms/OpenPepXLLF.xml                  |  1 +
 tools/openms/OpenSwathAnalyzer.xml            |  6 +++--
 tools/openms/OpenSwathAssayGenerator.xml      |  1 +
 .../openms/OpenSwathChromatogramExtractor.xml |  6 +++--
 tools/openms/OpenSwathConfidenceScoring.xml   |  1 +
 tools/openms/OpenSwathDIAPreScoring.xml       | 13 +++++----
 tools/openms/OpenSwathDecoyGenerator.xml      |  1 +
 tools/openms/OpenSwathFeatureXMLToTSV.xml     |  6 +++--
 tools/openms/OpenSwathFileSplitter.xml        |  3 ++-
 tools/openms/OpenSwathMzMLFileCacher.xml      |  1 +
 tools/openms/OpenSwathRTNormalizer.xml        |  6 +++--
 tools/openms/OpenSwathRewriteToFeatureXML.xml |  1 +
 tools/openms/OpenSwathWorkflow.xml            |  1 +
 tools/openms/PSMFeatureExtractor.patch        | 27 ++++++++++---------
 tools/openms/PSMFeatureExtractor.xml          | 20 +++++++-------
 tools/openms/PTModel.xml                      |  1 +
 tools/openms/PeakPickerHiRes.xml              |  1 +
 tools/openms/PeakPickerIterative.xml          |  1 +
 tools/openms/PeakPickerWavelet.xml            |  1 +
 tools/openms/PepNovoAdapter.patch             |  4 +--
 tools/openms/PepNovoAdapter.xml               |  1 +
 tools/openms/PeptideIndexer.xml               |  1 +
 tools/openms/PercolatorAdapter.xml            | 11 +++++---
 tools/openms/PhosphoScoring.xml               |  1 +
 tools/openms/PrecursorIonSelector.xml         |  1 +
 tools/openms/PrecursorMassCorrector.xml       |  1 +
 tools/openms/ProteinInference.xml             |  6 +++--
 tools/openms/ProteinQuantifier.xml            |  1 +
 tools/openms/ProteinResolver.xml              |  6 +++--
 tools/openms/QCCalculator.xml                 |  1 +
 tools/openms/QCEmbedder.xml                   |  1 +
 tools/openms/QCExporter.xml                   |  1 +
 tools/openms/QCExtractor.xml                  |  1 +
 tools/openms/QCImporter.xml                   |  1 +
 tools/openms/QCMerger.xml                     |  6 +++--
 tools/openms/QCShrinker.xml                   |  1 +
 tools/openms/QualityControl.xml               | 23 +++++++++-------
 tools/openms/RNADigestor.xml                  |  1 +
 tools/openms/RNAMassCalculator.xml            |  1 +
 tools/openms/RNPxlSearch.xml                  |  1 +
 tools/openms/RNPxlXICFilter.xml               |  1 +
 tools/openms/RTEvaluation.xml                 |  1 +
 tools/openms/RTModel.xml                      |  1 +
 tools/openms/SeedListGenerator.xml            |  1 +
 tools/openms/SemanticValidator.xml            |  6 +++--
 tools/openms/SequenceCoverageCalculator.xml   |  1 +
 tools/openms/SimpleSearchEngine.xml           |  1 +
 tools/openms/SiriusAdapter.xml                |  3 ++-
 tools/openms/SpecLibCreator.xml               |  1 +
 tools/openms/SpecLibSearcher.xml              | 13 +++++----
 tools/openms/SpectraFilterBernNorm.xml        |  1 +
 tools/openms/SpectraFilterMarkerMower.xml     |  1 +
 tools/openms/SpectraFilterNLargest.xml        |  1 +
 tools/openms/SpectraFilterNormalizer.xml      |  1 +
 tools/openms/SpectraFilterParentPeakMower.xml |  1 +
 tools/openms/SpectraFilterScaler.xml          |  1 +
 tools/openms/SpectraFilterSqrtMower.xml       |  1 +
 tools/openms/SpectraFilterThresholdMower.xml  |  1 +
 tools/openms/SpectraFilterWindowMower.xml     |  1 +
 tools/openms/SpectraMerger.xml                |  1 +
 tools/openms/SpectraSTSearchAdapter.xml       | 13 +++++----
 tools/openms/StaticModification.xml           |  1 +
 ...SvmTheoreticalSpectrumGeneratorTrainer.xml |  1 +
 tools/openms/TICCalculator.xml                |  1 +
 tools/openms/TOFCalibration.xml               |  1 +
 tools/openms/TargetedFileConverter.xml        |  1 +
 tools/openms/TextExporter.xml                 |  1 +
 tools/openms/TransformationEvaluation.xml     |  1 +
 tools/openms/XFDR.xml                         |  1 +
 tools/openms/XMLValidator.xml                 |  1 +
 tools/openms/XTandemAdapter.xml               |  1 +
 tools/openms/macros_autotest.xml              |  2 +-
 tools/openms/macros_test.xml                  |  9 +++----
 tools/openms/readme.md                        | 11 +++++---
 170 files changed, 389 insertions(+), 165 deletions(-)

diff --git a/tools/openms/404-urls.patch b/tools/openms/404-urls.patch
index f16870c07..169217b02 100644
--- a/tools/openms/404-urls.patch
+++ b/tools/openms/404-urls.patch
@@ -1,7 +1,7 @@
 diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml
 --- FeatureFinderSuperHirn.xml	2020-10-02 12:06:56.398572301 +0200
 +++ FeatureFinderSuperHirn.xml	2020-10-02 12:07:31.511153834 +0200
-@@ -105,6 +105,6 @@
+@@ -106,6 +106,6 @@
    <help><![CDATA[Finds mass spectrometric features in mass spectra.
  
  
diff --git a/tools/openms/AccurateMassSearch.xml b/tools/openms/AccurateMassSearch.xml
index 68a058faf..fa09ecfad 100644
--- a/tools/openms/AccurateMassSearch.xml
+++ b/tools/openms/AccurateMassSearch.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
@@ -32,11 +33,13 @@ mkdir out &&
 #end if
 #if $db.mapping:
   mkdir db.mapping &&
-  ${ ' '.join(["ln -s '%s' 'db.mapping/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _]) }
+  mkdir ${' '.join(["'db.mapping/%s'"%(os.path.basename(str(_))[:-4]) for _ in $db.mapping if _])} && 
+  ${' '.join(["ln -s '%s' 'db.mapping/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])}
 #end if
 #if $db.struct:
   mkdir db.struct &&
-  ${ ' '.join(["ln -s '%s' 'db.struct/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _]) }
+  mkdir ${' '.join(["'db.struct/%s'"%(os.path.basename(str(_))[:-4]) for _ in $db.struct if _])} && 
+  ${' '.join(["ln -s '%s' 'db.struct/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])}
 #end if
 
 ## Main program call
@@ -63,11 +66,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 #end if
 #if $db.mapping:
   -db:mapping
-  ${' '.join(["'db.mapping/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])}
+  ${' '.join(["'db.mapping/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])}
 #end if
 #if $db.struct:
   -db:struct
-  ${' '.join(["'db.struct/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])}
+  ${' '.join(["'db.struct/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])}
 #end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
diff --git a/tools/openms/AssayGeneratorMetabo.xml b/tools/openms/AssayGeneratorMetabo.xml
index 865b0ae9a..a0d7e0287 100644
--- a/tools/openms/AssayGeneratorMetabo.xml
+++ b/tools/openms/AssayGeneratorMetabo.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Assay library generation from DDA data (Metabolomics)</description>
   <macros>
     <token name="@EXECUTABLE@">AssayGeneratorMetabo</token>
@@ -14,12 +14,15 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir in_id &&
-${ ' '.join(["ln -s '%s' 'in_id/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _]) }
+mkdir ${' '.join(["'in_id/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_id if _])} && 
+${' '.join(["ln -s '%s' 'in_id/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _])}
 mkdir out &&
 
 ## Main program call
@@ -29,9 +32,9 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -in_id
-${' '.join(["'in_id/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _])}
+${' '.join(["'in_id/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _])}
 -out
 'out/output.${out_type}'
 
diff --git a/tools/openms/BaselineFilter.xml b/tools/openms/BaselineFilter.xml
index 167690d3a..bf41c6f85 100644
--- a/tools/openms/BaselineFilter.xml
+++ b/tools/openms/BaselineFilter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/CVInspector.xml b/tools/openms/CVInspector.xml
index afd3b9ffe..4582a1b49 100644
--- a/tools/openms/CVInspector.xml
+++ b/tools/openms/CVInspector.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir cv_files &&
-${ ' '.join(["ln -s '%s' 'cv_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _]) }
+mkdir ${' '.join(["'cv_files/%s'"%(os.path.basename(str(_))[:-4]) for _ in $cv_files if _])} && 
+${' '.join(["ln -s '%s' 'cv_files/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])}
 #if $mapping_file:
   mkdir mapping_file &&
   ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
@@ -33,7 +35,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -cv_files
-${' '.join(["'cv_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])}
+${' '.join(["'cv_files/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])}
 #if $mapping_file:
   -mapping_file
   'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
diff --git a/tools/openms/ClusterMassTraces.xml b/tools/openms/ClusterMassTraces.xml
index cc94192c6..0503cf946 100644
--- a/tools/openms/ClusterMassTraces.xml
+++ b/tools/openms/ClusterMassTraces.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/ClusterMassTracesByPrecursor.xml b/tools/openms/ClusterMassTracesByPrecursor.xml
index f92d0acd8..b786e8a06 100644
--- a/tools/openms/ClusterMassTracesByPrecursor.xml
+++ b/tools/openms/ClusterMassTracesByPrecursor.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_ms1 &&
diff --git a/tools/openms/CometAdapter.xml b/tools/openms/CometAdapter.xml
index 798a6bb2d..e608fbba3 100644
--- a/tools/openms/CometAdapter.xml
+++ b/tools/openms/CometAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/CompNovo.xml b/tools/openms/CompNovo.xml
index c505a6f7b..c59060903 100644
--- a/tools/openms/CompNovo.xml
+++ b/tools/openms/CompNovo.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/CompNovoCID.xml b/tools/openms/CompNovoCID.xml
index 76ab3befe..aa467bcd4 100644
--- a/tools/openms/CompNovoCID.xml
+++ b/tools/openms/CompNovoCID.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/ConsensusID.xml b/tools/openms/ConsensusID.xml
index e8f3b68c7..0ea85bfd7 100644
--- a/tools/openms/ConsensusID.xml
+++ b/tools/openms/ConsensusID.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 
 ## Main program call
@@ -27,7 +29,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${in[0].ext}'
 
diff --git a/tools/openms/ConsensusMapNormalizer.xml b/tools/openms/ConsensusMapNormalizer.xml
index 9a680b076..600ddb4b0 100644
--- a/tools/openms/ConsensusMapNormalizer.xml
+++ b/tools/openms/ConsensusMapNormalizer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/CruxAdapter.xml b/tools/openms/CruxAdapter.xml
index 3b614923f..d6899d77c 100644
--- a/tools/openms/CruxAdapter.xml
+++ b/tools/openms/CruxAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/DTAExtractor.xml b/tools/openms/DTAExtractor.xml
index 72a1611cd..c4ae4a202 100644
--- a/tools/openms/DTAExtractor.xml
+++ b/tools/openms/DTAExtractor.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/DatabaseFilter.xml b/tools/openms/DatabaseFilter.xml
index 1c7d39908..1786771be 100644
--- a/tools/openms/DatabaseFilter.xml
+++ b/tools/openms/DatabaseFilter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/DatabaseSuitability.xml b/tools/openms/DatabaseSuitability.xml
index 695555361..9be7379a1 100644
--- a/tools/openms/DatabaseSuitability.xml
+++ b/tools/openms/DatabaseSuitability.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_id &&
diff --git a/tools/openms/DeMeanderize.xml b/tools/openms/DeMeanderize.xml
index ff8e4606e..d5b3593c0 100644
--- a/tools/openms/DeMeanderize.xml
+++ b/tools/openms/DeMeanderize.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/Decharger.xml b/tools/openms/Decharger.xml
index 704fc8c09..35bec4f43 100644
--- a/tools/openms/Decharger.xml
+++ b/tools/openms/Decharger.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/DecoyDatabase.xml b/tools/openms/DecoyDatabase.xml
index 6500aac06..d96d1cf16 100644
--- a/tools/openms/DecoyDatabase.xml
+++ b/tools/openms/DecoyDatabase.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 
 ## Main program call
@@ -27,7 +29,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${gxy2omsext("fasta")}'
 
diff --git a/tools/openms/Digestor.xml b/tools/openms/Digestor.xml
index c7ab245af..eced9b291 100644
--- a/tools/openms/Digestor.xml
+++ b/tools/openms/Digestor.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/DigestorMotif.xml b/tools/openms/DigestorMotif.xml
index 633450ff6..5d5dddd92 100644
--- a/tools/openms/DigestorMotif.xml
+++ b/tools/openms/DigestorMotif.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/EICExtractor.xml b/tools/openms/EICExtractor.xml
index db2d8bc8b..6e3b36116 100644
--- a/tools/openms/EICExtractor.xml
+++ b/tools/openms/EICExtractor.xml
@@ -14,13 +14,16 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if $in_header:
   mkdir in_header &&
-  ${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) }
+  mkdir ${' '.join(["'in_header/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_header if _])} && 
+  ${' '.join(["ln -s '%s' 'in_header/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])}
 #end if
 mkdir pos &&
 ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
@@ -36,10 +39,10 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if $in_header:
   -in_header
-  ${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])}
+  ${' '.join(["'in_header/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])}
 #end if
 -pos
 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)'
diff --git a/tools/openms/ERPairFinder.xml b/tools/openms/ERPairFinder.xml
index 5006db915..7cbc363b1 100644
--- a/tools/openms/ERPairFinder.xml
+++ b/tools/openms/ERPairFinder.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/Epifany.xml b/tools/openms/Epifany.xml
index c3cbc9357..ca0a619a8 100644
--- a/tools/openms/Epifany.xml
+++ b/tools/openms/Epifany.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if $exp_design:
   mkdir exp_design &&
   ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' &&
@@ -31,7 +33,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if $exp_design:
   -exp_design
   'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)'
diff --git a/tools/openms/ExternalCalibration.xml b/tools/openms/ExternalCalibration.xml
index 6ac96a093..41f92db4d 100644
--- a/tools/openms/ExternalCalibration.xml
+++ b/tools/openms/ExternalCalibration.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FFEval.xml b/tools/openms/FFEval.xml
index 496d81615..f91d8faec 100644
--- a/tools/openms/FFEval.xml
+++ b/tools/openms/FFEval.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FalseDiscoveryRate.xml b/tools/openms/FalseDiscoveryRate.xml
index 72127b1a2..8d9d3b6f0 100644
--- a/tools/openms/FalseDiscoveryRate.xml
+++ b/tools/openms/FalseDiscoveryRate.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderCentroided.xml b/tools/openms/FeatureFinderCentroided.xml
index f93548d99..7f05244b3 100644
--- a/tools/openms/FeatureFinderCentroided.xml
+++ b/tools/openms/FeatureFinderCentroided.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderIdentification.xml b/tools/openms/FeatureFinderIdentification.xml
index 8d017f874..0ac18ddae 100644
--- a/tools/openms/FeatureFinderIdentification.xml
+++ b/tools/openms/FeatureFinderIdentification.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderIsotopeWavelet.xml b/tools/openms/FeatureFinderIsotopeWavelet.xml
index e77b2bf0c..147c6ce9a 100644
--- a/tools/openms/FeatureFinderIsotopeWavelet.xml
+++ b/tools/openms/FeatureFinderIsotopeWavelet.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderMRM.xml b/tools/openms/FeatureFinderMRM.xml
index c37f578f8..1063604fd 100644
--- a/tools/openms/FeatureFinderMRM.xml
+++ b/tools/openms/FeatureFinderMRM.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderMetabo.xml b/tools/openms/FeatureFinderMetabo.xml
index 869e0dca0..1ee928c94 100644
--- a/tools/openms/FeatureFinderMetabo.xml
+++ b/tools/openms/FeatureFinderMetabo.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderMetaboIdent.xml b/tools/openms/FeatureFinderMetaboIdent.xml
index 262fface7..ba98344a6 100644
--- a/tools/openms/FeatureFinderMetaboIdent.xml
+++ b/tools/openms/FeatureFinderMetaboIdent.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderMultiplex.xml b/tools/openms/FeatureFinderMultiplex.xml
index c985a3caa..b26e03943 100644
--- a/tools/openms/FeatureFinderMultiplex.xml
+++ b/tools/openms/FeatureFinderMultiplex.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureFinderSuperHirn.xml b/tools/openms/FeatureFinderSuperHirn.xml
index 7077691a7..d4b3fcbed 100644
--- a/tools/openms/FeatureFinderSuperHirn.xml
+++ b/tools/openms/FeatureFinderSuperHirn.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureLinkerLabeled.xml b/tools/openms/FeatureLinkerLabeled.xml
index f1961da8c..326905e36 100644
--- a/tools/openms/FeatureLinkerLabeled.xml
+++ b/tools/openms/FeatureLinkerLabeled.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FeatureLinkerUnlabeled.xml b/tools/openms/FeatureLinkerUnlabeled.xml
index 8ffc38a96..0778a3f0d 100644
--- a/tools/openms/FeatureLinkerUnlabeled.xml
+++ b/tools/openms/FeatureLinkerUnlabeled.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 #if $design:
   mkdir design &&
@@ -31,7 +33,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${gxy2omsext("consensusxml")}'
 #if $design:
diff --git a/tools/openms/FeatureLinkerUnlabeledKD.xml b/tools/openms/FeatureLinkerUnlabeledKD.xml
index 515fda885..c965e840b 100644
--- a/tools/openms/FeatureLinkerUnlabeledKD.xml
+++ b/tools/openms/FeatureLinkerUnlabeledKD.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 #if $design:
   mkdir design &&
@@ -31,7 +33,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${gxy2omsext("consensusxml")}'
 #if $design:
diff --git a/tools/openms/FeatureLinkerUnlabeledQT.xml b/tools/openms/FeatureLinkerUnlabeledQT.xml
index 5e0adffce..a1b0f8f2a 100644
--- a/tools/openms/FeatureLinkerUnlabeledQT.xml
+++ b/tools/openms/FeatureLinkerUnlabeledQT.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 #if $design:
   mkdir design &&
@@ -31,7 +33,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${gxy2omsext("consensusxml")}'
 #if $design:
diff --git a/tools/openms/FidoAdapter.xml b/tools/openms/FidoAdapter.xml
index 8c62dcaf8..fba5ef281 100644
--- a/tools/openms/FidoAdapter.xml
+++ b/tools/openms/FidoAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FileConverter.xml b/tools/openms/FileConverter.xml
index d13e90ce8..cdbee8fc8 100644
--- a/tools/openms/FileConverter.xml
+++ b/tools/openms/FileConverter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FileFilter.xml b/tools/openms/FileFilter.xml
index eb19cfcbf..c9e66d85c 100644
--- a/tools/openms/FileFilter.xml
+++ b/tools/openms/FileFilter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FileInfo.xml b/tools/openms/FileInfo.xml
index 6d5c9aa75..89f40aa79 100644
--- a/tools/openms/FileInfo.xml
+++ b/tools/openms/FileInfo.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/FileMerger.xml b/tools/openms/FileMerger.xml
index 1dfbfec00..e041e3b0e 100644
--- a/tools/openms/FileMerger.xml
+++ b/tools/openms/FileMerger.xml
@@ -14,13 +14,16 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir rt_concat_trafo_out &&
+  mkdir ${' '.join(["'rt_concat_trafo_out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 
 ## Main program call
@@ -30,12 +33,12 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${out_type}'
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -rt_concat:trafo_out
-  ${' '.join(["'rt_concat_trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
+  ${' '.join(["'rt_concat_trafo_out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
 #end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
@@ -44,7 +47,7 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
 ## Postprocessing
 && mv 'out/output.${out_type}' '$out'
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $rt_concat_trafo_out if _])}
+  ${' '.join(["&& mv -n 'rt_concat_trafo_out/%(bn)s/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $in if _])}
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -101,7 +104,7 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
       </change_format>
     </data>
     <collection type="list" name="rt_concat_trafo_out" label="${tool.name} on ${on_string}: rt_concat:trafo_out">
-      <discover_datasets directory="rt_concat.trafo_out" format="trafoxml" pattern="__name__"/>
+      <discover_datasets directory="rt_concat_trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
diff --git a/tools/openms/FuzzyDiff.xml b/tools/openms/FuzzyDiff.xml
index da1355bef..45a68d1fb 100644
--- a/tools/openms/FuzzyDiff.xml
+++ b/tools/openms/FuzzyDiff.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in1 &&
diff --git a/tools/openms/GNPSExport.xml b/tools/openms/GNPSExport.xml
index 5c47ce4cd..edfae733d 100644
--- a/tools/openms/GNPSExport.xml
+++ b/tools/openms/GNPSExport.xml
@@ -14,12 +14,14 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_cm &&
 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
 mkdir in_mzml &&
-${ ' '.join(["ln -s '%s' 'in_mzml/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _]) }
+mkdir ${' '.join(["'in_mzml/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_mzml if _])} && 
+${' '.join(["ln -s '%s' 'in_mzml/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _])}
 mkdir out &&
 
 ## Main program call
@@ -31,7 +33,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 -in_cm
 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
 -in_mzml
-${' '.join(["'in_mzml/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _])}
+${' '.join(["'in_mzml/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _])}
 -out
 'out/output.${gxy2omsext("mgf")}'
 
diff --git a/tools/openms/HighResPrecursorMassCorrector.xml b/tools/openms/HighResPrecursorMassCorrector.xml
index fcddec0ea..a926b538a 100644
--- a/tools/openms/HighResPrecursorMassCorrector.xml
+++ b/tools/openms/HighResPrecursorMassCorrector.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDConflictResolver.xml b/tools/openms/IDConflictResolver.xml
index b848ddeb8..ae8a0f736 100644
--- a/tools/openms/IDConflictResolver.xml
+++ b/tools/openms/IDConflictResolver.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDExtractor.xml b/tools/openms/IDExtractor.xml
index 8ef64c367..2b65a466f 100644
--- a/tools/openms/IDExtractor.xml
+++ b/tools/openms/IDExtractor.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDFileConverter.xml b/tools/openms/IDFileConverter.xml
index f6e28984e..a67c971ec 100644
--- a/tools/openms/IDFileConverter.xml
+++ b/tools/openms/IDFileConverter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDFilter.xml b/tools/openms/IDFilter.xml
index 0f9d2b99c..3c435c7c7 100644
--- a/tools/openms/IDFilter.xml
+++ b/tools/openms/IDFilter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDMapper.xml b/tools/openms/IDMapper.xml
index 11c509775..cb6508cfa 100644
--- a/tools/openms/IDMapper.xml
+++ b/tools/openms/IDMapper.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir id &&
diff --git a/tools/openms/IDMassAccuracy.xml b/tools/openms/IDMassAccuracy.xml
index 0673868fd..4d5366d63 100644
--- a/tools/openms/IDMassAccuracy.xml
+++ b/tools/openms/IDMassAccuracy.xml
@@ -14,12 +14,15 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir id_in &&
-${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
+mkdir ${' '.join(["'id_in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $id_in if _])} && 
+${' '.join(["ln -s '%s' 'id_in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_precursor &&
 #end if
@@ -40,9 +43,9 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -id_in
-${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
+${' '.join(["'id_in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_precursor
   'out_precursor/output.${gxy2omsext("tabular")}'
diff --git a/tools/openms/IDMerger.xml b/tools/openms/IDMerger.xml
index c8b593344..0e470e59e 100644
--- a/tools/openms/IDMerger.xml
+++ b/tools/openms/IDMerger.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 #if $add_to:
   mkdir add_to &&
@@ -31,7 +33,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${gxy2omsext("idxml")}'
 #if $add_to:
diff --git a/tools/openms/IDPosteriorErrorProbability.xml b/tools/openms/IDPosteriorErrorProbability.xml
index efeef2da7..3d27ee1b7 100644
--- a/tools/openms/IDPosteriorErrorProbability.xml
+++ b/tools/openms/IDPosteriorErrorProbability.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDRTCalibration.xml b/tools/openms/IDRTCalibration.xml
index 3d308e577..85b29e846 100644
--- a/tools/openms/IDRTCalibration.xml
+++ b/tools/openms/IDRTCalibration.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDRipper.xml b/tools/openms/IDRipper.xml
index 90f4eccd0..0177b8c54 100644
--- a/tools/openms/IDRipper.xml
+++ b/tools/openms/IDRipper.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
@@ -53,7 +54,7 @@ out_path/
   </inputs>
   <outputs>
     <collection type="list" name="out_path" label="${tool.name} on ${on_string}: out_path">
-      <discover_datasets directory="out_path" format="idxml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+      <discover_datasets directory="out_path" recurse="true" format="idxml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
diff --git a/tools/openms/IDScoreSwitcher.xml b/tools/openms/IDScoreSwitcher.xml
index cc22867c5..b1d41a113 100644
--- a/tools/openms/IDScoreSwitcher.xml
+++ b/tools/openms/IDScoreSwitcher.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IDSplitter.xml b/tools/openms/IDSplitter.xml
index 82e58cfc2..ee04408c8 100644
--- a/tools/openms/IDSplitter.xml
+++ b/tools/openms/IDSplitter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/InternalCalibration.xml b/tools/openms/InternalCalibration.xml
index a05c968bf..611596603 100644
--- a/tools/openms/InternalCalibration.xml
+++ b/tools/openms/InternalCalibration.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/IsobaricAnalyzer.xml b/tools/openms/IsobaricAnalyzer.xml
index 1b44bab96..1e6f4d01b 100644
--- a/tools/openms/IsobaricAnalyzer.xml
+++ b/tools/openms/IsobaricAnalyzer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/LabeledEval.xml b/tools/openms/LabeledEval.xml
index 0c4143a35..b7099ef56 100644
--- a/tools/openms/LabeledEval.xml
+++ b/tools/openms/LabeledEval.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/LuciphorAdapter.xml b/tools/openms/LuciphorAdapter.xml
index c72ebd3cb..554a3bb79 100644
--- a/tools/openms/LuciphorAdapter.xml
+++ b/tools/openms/LuciphorAdapter.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Modification site localisation using LuciPHOr2.</description>
   <macros>
     <token name="@EXECUTABLE@">LuciphorAdapter</token>
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MRMMapper.xml b/tools/openms/MRMMapper.xml
index 0ca05ab98..f4a64d0df 100644
--- a/tools/openms/MRMMapper.xml
+++ b/tools/openms/MRMMapper.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MRMPairFinder.xml b/tools/openms/MRMPairFinder.xml
index 0489eae41..1bef4aa66 100644
--- a/tools/openms/MRMPairFinder.xml
+++ b/tools/openms/MRMPairFinder.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MRMTransitionGroupPicker.xml b/tools/openms/MRMTransitionGroupPicker.xml
index 0e57dc6a6..22035f5bc 100644
--- a/tools/openms/MRMTransitionGroupPicker.xml
+++ b/tools/openms/MRMTransitionGroupPicker.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MSFraggerAdapter.xml b/tools/openms/MSFraggerAdapter.xml
index 90051e774..03445aabf 100644
--- a/tools/openms/MSFraggerAdapter.xml
+++ b/tools/openms/MSFraggerAdapter.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Peptide Identification with MSFragger</description>
   <macros>
     <token name="@EXECUTABLE@">MSFraggerAdapter</token>
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MSGFPlusAdapter.xml b/tools/openms/MSGFPlusAdapter.xml
index 40ae8141d..090f62060 100644
--- a/tools/openms/MSGFPlusAdapter.xml
+++ b/tools/openms/MSGFPlusAdapter.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Identification]-->
-<tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>MS/MS database search using MS-GF+.</description>
   <macros>
     <token name="@EXECUTABLE@">MSGFPlusAdapter</token>
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MSSimulator.xml b/tools/openms/MSSimulator.xml
index cb620bd67..94adecfff 100644
--- a/tools/openms/MSSimulator.xml
+++ b/tools/openms/MSSimulator.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -47,7 +49,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
   'out/output.${gxy2omsext("mzml")}'
diff --git a/tools/openms/MSstatsConverter.xml b/tools/openms/MSstatsConverter.xml
index e0ac0ec06..aca575e0b 100644
--- a/tools/openms/MSstatsConverter.xml
+++ b/tools/openms/MSstatsConverter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
@@ -24,7 +25,8 @@ mkdir out &&
 #if $adv_opts_cond.adv_opts_selector=='advanced':
   #if $adv_opts_cond.reannotate_filenames:
     mkdir adv_opts_cond.reannotate_filenames &&
-    ${ ' '.join(["ln -s '%s' 'adv_opts_cond.reannotate_filenames/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _]) }
+    mkdir ${' '.join(["'adv_opts_cond.reannotate_filenames/%s'"%(os.path.basename(str(_))[:-4]) for _ in $adv_opts_cond.reannotate_filenames if _])} && 
+    ${' '.join(["ln -s '%s' 'adv_opts_cond.reannotate_filenames/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _])}
   #end if
 #end if
 
@@ -43,7 +45,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 #if $adv_opts_cond.adv_opts_selector=='advanced':
   #if $adv_opts_cond.reannotate_filenames:
     -reannotate_filenames
-    ${' '.join(["'adv_opts_cond.reannotate_filenames/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _])}
+    ${' '.join(["'adv_opts_cond.reannotate_filenames/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _])}
   #end if
 #end if
 
diff --git a/tools/openms/MaRaClusterAdapter.xml b/tools/openms/MaRaClusterAdapter.xml
index a9d1a1258..d99a81826 100644
--- a/tools/openms/MaRaClusterAdapter.xml
+++ b/tools/openms/MaRaClusterAdapter.xml
@@ -14,13 +14,16 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if $id_in:
   mkdir id_in &&
-  ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
+  mkdir ${' '.join(["'id_in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $id_in if _])} && 
+  ${' '.join(["ln -s '%s' 'id_in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -33,10 +36,10 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if $id_in:
   -id_in
-  ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
+  ${' '.join(["'id_in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
diff --git a/tools/openms/MapAlignerIdentification.xml b/tools/openms/MapAlignerIdentification.xml
index 799dc350a..77a96e51d 100644
--- a/tools/openms/MapAlignerIdentification.xml
+++ b/tools/openms/MapAlignerIdentification.xml
@@ -14,15 +14,19 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
+  mkdir ${' '.join(["'out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
+  mkdir ${' '.join(["'trafo_out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 #if $design:
   mkdir design &&
@@ -40,14 +44,14 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
-  ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
+  ${' '.join(["'out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -trafo_out
-  ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
+  ${' '.join(["'trafo_out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
 #end if
 #if $design:
   -design
@@ -63,7 +67,7 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
 
 ## Postprocessing
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
+  ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $in if _])}
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -176,11 +180,11 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" pattern="__name_and_ext__"/>
+      <discover_datasets directory="out" recurse="true" pattern="__name_and_ext__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
-      <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
+      <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
diff --git a/tools/openms/MapAlignerPoseClustering.xml b/tools/openms/MapAlignerPoseClustering.xml
index a13850d82..b2b4291a1 100644
--- a/tools/openms/MapAlignerPoseClustering.xml
+++ b/tools/openms/MapAlignerPoseClustering.xml
@@ -14,15 +14,19 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
+  mkdir ${' '.join(["'out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
+  mkdir ${' '.join(["'trafo_out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 #if $reference.file:
   mkdir reference.file &&
@@ -36,14 +40,14 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
-  ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
+  ${' '.join(["'out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])}
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -trafo_out
-  ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
+  ${' '.join(["'trafo_out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
 #end if
 #if $reference.file:
   -reference:file
@@ -55,7 +59,7 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
 
 ## Postprocessing
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
+  ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $in if _])}
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -132,11 +136,11 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" pattern="__name_and_ext__"/>
+      <discover_datasets directory="out" recurse="true" pattern="__name_and_ext__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
-      <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
+      <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
diff --git a/tools/openms/MapAlignerSpectrum.xml b/tools/openms/MapAlignerSpectrum.xml
index 25c891f0e..d2788774f 100644
--- a/tools/openms/MapAlignerSpectrum.xml
+++ b/tools/openms/MapAlignerSpectrum.xml
@@ -14,15 +14,19 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
+  mkdir ${' '.join(["'out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
+  mkdir ${' '.join(["'trafo_out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 
 ## Main program call
@@ -32,14 +36,14 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
-  ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("mzml")) for _ in $in if _])}
+  ${' '.join(["'out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("mzml")) for _ in $in if _])}
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -trafo_out
-  ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
+  ${' '.join(["'trafo_out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
 #end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
@@ -47,10 +51,10 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
 
 ## Postprocessing
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("mzml")} for _ in $out if _])}
+  ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("mzml")} for _ in $in if _])}
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
+  ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $in if _])}
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -163,11 +167,11 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" format="mzml" pattern="__name__"/>
+      <discover_datasets directory="out" recurse="true" format="mzml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
-      <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
+      <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
diff --git a/tools/openms/MapAlignerTreeGuided.xml b/tools/openms/MapAlignerTreeGuided.xml
index 4ba63cca4..1066538f7 100644
--- a/tools/openms/MapAlignerTreeGuided.xml
+++ b/tools/openms/MapAlignerTreeGuided.xml
@@ -14,15 +14,19 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
+  mkdir ${' '.join(["'out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir trafo_out &&
+  mkdir ${' '.join(["'trafo_out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 #end if
 
 ## Main program call
@@ -32,14 +36,14 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
-  ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in if _])}
+  ${' '.join(["'out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in if _])}
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -trafo_out
-  ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
+  ${' '.join(["'trafo_out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
 #end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
@@ -47,10 +51,10 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
 
 ## Postprocessing
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $out if _])}
+  ${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $in if _])}
 #end if
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
+  ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $in if _])}
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -167,11 +171,11 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" format="featurexml" pattern="__name__"/>
+      <discover_datasets directory="out" recurse="true" format="featurexml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
-      <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
+      <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
diff --git a/tools/openms/MapNormalizer.xml b/tools/openms/MapNormalizer.xml
index b369e20bd..ccd9a05eb 100644
--- a/tools/openms/MapNormalizer.xml
+++ b/tools/openms/MapNormalizer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MapRTTransformer.xml b/tools/openms/MapRTTransformer.xml
index bc21012ad..b9ecac83e 100644
--- a/tools/openms/MapRTTransformer.xml
+++ b/tools/openms/MapRTTransformer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/MapStatistics.xml b/tools/openms/MapStatistics.xml
index b4a0e2dc5..e7a3a1a19 100644
--- a/tools/openms/MapStatistics.xml
+++ b/tools/openms/MapStatistics.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MascotAdapter.xml b/tools/openms/MascotAdapter.xml
index 3a6a7e975..6ddf00f92 100644
--- a/tools/openms/MascotAdapter.xml
+++ b/tools/openms/MascotAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MascotAdapterOnline.xml b/tools/openms/MascotAdapterOnline.xml
index b815a6729..69970f8ea 100644
--- a/tools/openms/MascotAdapterOnline.xml
+++ b/tools/openms/MascotAdapterOnline.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MassCalculator.xml b/tools/openms/MassCalculator.xml
index 6a1ad76fc..cc4b3ce3d 100644
--- a/tools/openms/MassCalculator.xml
+++ b/tools/openms/MassCalculator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/MassTraceExtractor.xml b/tools/openms/MassTraceExtractor.xml
index 5173e3efc..4ab7278e2 100644
--- a/tools/openms/MassTraceExtractor.xml
+++ b/tools/openms/MassTraceExtractor.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MetaProSIP.xml b/tools/openms/MetaProSIP.xml
index e09c75762..950ad3020 100644
--- a/tools/openms/MetaProSIP.xml
+++ b/tools/openms/MetaProSIP.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_mzML &&
diff --git a/tools/openms/MetaboliteAdductDecharger.xml b/tools/openms/MetaboliteAdductDecharger.xml
index 1e81ef5c2..8d522c3e0 100644
--- a/tools/openms/MetaboliteAdductDecharger.xml
+++ b/tools/openms/MetaboliteAdductDecharger.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MetaboliteSpectralMatcher.xml b/tools/openms/MetaboliteSpectralMatcher.xml
index e87c94093..636dce6ab 100644
--- a/tools/openms/MetaboliteSpectralMatcher.xml
+++ b/tools/openms/MetaboliteSpectralMatcher.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MultiplexResolver.xml b/tools/openms/MultiplexResolver.xml
index 8cadf99b5..6157198eb 100644
--- a/tools/openms/MultiplexResolver.xml
+++ b/tools/openms/MultiplexResolver.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MyriMatchAdapter.xml b/tools/openms/MyriMatchAdapter.xml
index e11a80c91..8291c4b8e 100644
--- a/tools/openms/MyriMatchAdapter.xml
+++ b/tools/openms/MyriMatchAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/MzMLSplitter.xml b/tools/openms/MzMLSplitter.xml
index 9c7f41535..855b3b2c3 100644
--- a/tools/openms/MzMLSplitter.xml
+++ b/tools/openms/MzMLSplitter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
@@ -63,7 +64,7 @@ out/
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+      <discover_datasets directory="out" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
diff --git a/tools/openms/MzTabExporter.xml b/tools/openms/MzTabExporter.xml
index 50c3b6e3c..5a35e4101 100644
--- a/tools/openms/MzTabExporter.xml
+++ b/tools/openms/MzTabExporter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/NoiseFilterGaussian.xml b/tools/openms/NoiseFilterGaussian.xml
index 751adeef4..c469c8ce7 100644
--- a/tools/openms/NoiseFilterGaussian.xml
+++ b/tools/openms/NoiseFilterGaussian.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/NoiseFilterSGolay.xml b/tools/openms/NoiseFilterSGolay.xml
index 5b2fff89f..89b30bf33 100644
--- a/tools/openms/NoiseFilterSGolay.xml
+++ b/tools/openms/NoiseFilterSGolay.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/NovorAdapter.xml b/tools/openms/NovorAdapter.xml
index 590c83517..9c2650eb1 100644
--- a/tools/openms/NovorAdapter.xml
+++ b/tools/openms/NovorAdapter.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Template for Tool creation</description>
   <macros>
     <token name="@EXECUTABLE@">NovorAdapter</token>
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/NucleicAcidSearchEngine.xml b/tools/openms/NucleicAcidSearchEngine.xml
index f914a7cf9..ff3cc440f 100644
--- a/tools/openms/NucleicAcidSearchEngine.xml
+++ b/tools/openms/NucleicAcidSearchEngine.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OMSSAAdapter.patch b/tools/openms/OMSSAAdapter.patch
index 68439613b..6cdebd628 100644
--- a/tools/openms/OMSSAAdapter.patch
+++ b/tools/openms/OMSSAAdapter.patch
@@ -1,6 +1,6 @@
 --- OMSSAAdapter.xml	2020-06-16 15:51:40.315400730 +0200
 +++ /tmp/OMSSAAdapter.xml	2020-06-16 15:50:23.536086074 +0200
-@@ -22,6 +22,7 @@
+@@ -23,6 +23,7 @@
  mkdir database &&
  ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
  
diff --git a/tools/openms/OMSSAAdapter.xml b/tools/openms/OMSSAAdapter.xml
index 520642841..299944d7e 100644
--- a/tools/openms/OMSSAAdapter.xml
+++ b/tools/openms/OMSSAAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OpenPepXL.xml b/tools/openms/OpenPepXL.xml
index 48f88fdfd..c1068b1ea 100644
--- a/tools/openms/OpenPepXL.xml
+++ b/tools/openms/OpenPepXL.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OpenPepXLLF.xml b/tools/openms/OpenPepXLLF.xml
index 6491a2b4c..a11515b1e 100644
--- a/tools/openms/OpenPepXLLF.xml
+++ b/tools/openms/OpenPepXLLF.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OpenSwathAnalyzer.xml b/tools/openms/OpenSwathAnalyzer.xml
index 3ff57ce5e..8c00b3cd6 100644
--- a/tools/openms/OpenSwathAnalyzer.xml
+++ b/tools/openms/OpenSwathAnalyzer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
@@ -27,7 +28,8 @@ ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($
 mkdir out &&
 #if $swath_files:
   mkdir swath_files &&
-  ${ ' '.join(["ln -s '%s' 'swath_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _]) }
+  mkdir ${' '.join(["'swath_files/%s'"%(os.path.basename(str(_))[:-4]) for _ in $swath_files if _])} && 
+  ${' '.join(["ln -s '%s' 'swath_files/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
 #end if
 
 ## Main program call
@@ -48,7 +50,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 'out/output.${gxy2omsext("featurexml")}'
 #if $swath_files:
   -swath_files
-  ${' '.join(["'swath_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
+  ${' '.join(["'swath_files/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
 #end if
 
 ## Postprocessing
diff --git a/tools/openms/OpenSwathAssayGenerator.xml b/tools/openms/OpenSwathAssayGenerator.xml
index 73f6344ea..240e44bc6 100644
--- a/tools/openms/OpenSwathAssayGenerator.xml
+++ b/tools/openms/OpenSwathAssayGenerator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OpenSwathChromatogramExtractor.xml b/tools/openms/OpenSwathChromatogramExtractor.xml
index 9b85c1008..9011df2a2 100644
--- a/tools/openms/OpenSwathChromatogramExtractor.xml
+++ b/tools/openms/OpenSwathChromatogramExtractor.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir tr &&
 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 #if $rt_norm:
@@ -33,7 +35,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -tr
 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
 #if $rt_norm:
diff --git a/tools/openms/OpenSwathConfidenceScoring.xml b/tools/openms/OpenSwathConfidenceScoring.xml
index e9ffa95e3..d234bc416 100644
--- a/tools/openms/OpenSwathConfidenceScoring.xml
+++ b/tools/openms/OpenSwathConfidenceScoring.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OpenSwathDIAPreScoring.xml b/tools/openms/OpenSwathDIAPreScoring.xml
index ebe073d35..3973c7b11 100644
--- a/tools/openms/OpenSwathDIAPreScoring.xml
+++ b/tools/openms/OpenSwathDIAPreScoring.xml
@@ -14,13 +14,16 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir tr &&
 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir swath_files &&
-${ ' '.join(["ln -s '%s' 'swath_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _]) }
+mkdir ${' '.join(["'swath_files/%s'"%(os.path.basename(str(_))[:-4]) for _ in $swath_files if _])} && 
+${' '.join(["ln -s '%s' 'swath_files/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
 mkdir output_files &&
+mkdir ${' '.join(["'output_files/%s'"%(os.path.basename(str(_))[:-4]) for _ in $swath_files if _])} && 
 
 ## Main program call
 
@@ -31,12 +34,12 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 -tr
 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
 -swath_files
-${' '.join(["'swath_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
+${' '.join(["'swath_files/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
 -output_files
-${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("tabular")) for _ in $swath_files if _])}
+${' '.join(["'output_files/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("tabular")) for _ in $swath_files if _])}
 
 ## Postprocessing
-${' '.join(["&& mv -n 'swath_files/%(id)s.%(gext)s' 'output_files/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("tabular")} for _ in $output_files if _])}
+${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(gext)s' 'output_files/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("tabular")} for _ in $swath_files if _])}
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -60,7 +63,7 @@ ${' '.join(["&& mv -n 'swath_files/%(id)s.%(gext)s' 'output_files/%(id)s'"%{"id"
   </inputs>
   <outputs>
     <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
-      <discover_datasets directory="output_files" format="tabular" pattern="__name__"/>
+      <discover_datasets directory="output_files" recurse="true" format="tabular" pattern="__name__"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
diff --git a/tools/openms/OpenSwathDecoyGenerator.xml b/tools/openms/OpenSwathDecoyGenerator.xml
index fdf4144d3..14330328f 100644
--- a/tools/openms/OpenSwathDecoyGenerator.xml
+++ b/tools/openms/OpenSwathDecoyGenerator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OpenSwathFeatureXMLToTSV.xml b/tools/openms/OpenSwathFeatureXMLToTSV.xml
index dd3b16ae9..059b104ca 100644
--- a/tools/openms/OpenSwathFeatureXMLToTSV.xml
+++ b/tools/openms/OpenSwathFeatureXMLToTSV.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir tr &&
 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir out &&
@@ -29,7 +31,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -tr
 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
 -out
diff --git a/tools/openms/OpenSwathFileSplitter.xml b/tools/openms/OpenSwathFileSplitter.xml
index 2f2ffc098..7a3e8c534 100644
--- a/tools/openms/OpenSwathFileSplitter.xml
+++ b/tools/openms/OpenSwathFileSplitter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
@@ -67,7 +68,7 @@ outputDirectory/
   </inputs>
   <outputs>
     <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
-      <discover_datasets directory="outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+      <discover_datasets directory="outputDirectory" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
     <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
       <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
diff --git a/tools/openms/OpenSwathMzMLFileCacher.xml b/tools/openms/OpenSwathMzMLFileCacher.xml
index 868e18bfd..d31e1fd19 100644
--- a/tools/openms/OpenSwathMzMLFileCacher.xml
+++ b/tools/openms/OpenSwathMzMLFileCacher.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/OpenSwathRTNormalizer.xml b/tools/openms/OpenSwathRTNormalizer.xml
index 11d0ec5f6..ba2aaad22 100644
--- a/tools/openms/OpenSwathRTNormalizer.xml
+++ b/tools/openms/OpenSwathRTNormalizer.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir tr &&
 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir out &&
@@ -33,7 +35,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -tr
 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
 -out
diff --git a/tools/openms/OpenSwathRewriteToFeatureXML.xml b/tools/openms/OpenSwathRewriteToFeatureXML.xml
index 4ec7a686c..5e9b171a2 100644
--- a/tools/openms/OpenSwathRewriteToFeatureXML.xml
+++ b/tools/openms/OpenSwathRewriteToFeatureXML.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $csv:
diff --git a/tools/openms/OpenSwathWorkflow.xml b/tools/openms/OpenSwathWorkflow.xml
index bc743ec3e..1077ec5df 100644
--- a/tools/openms/OpenSwathWorkflow.xml
+++ b/tools/openms/OpenSwathWorkflow.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PSMFeatureExtractor.patch b/tools/openms/PSMFeatureExtractor.patch
index 6128b9548..38b89cc1a 100644
--- a/tools/openms/PSMFeatureExtractor.patch
+++ b/tools/openms/PSMFeatureExtractor.patch
@@ -1,35 +1,36 @@
---- PSMFeatureExtractor_org.xml	2020-12-13 17:31:30.509959130 +0100
-+++ PSMFeatureExtractor.xml	2020-12-13 17:32:16.500277367 +0100
-@@ -17,7 +17,11 @@
+--- PSMFeatureExtractor.xml.orig	2021-02-06 18:35:56.520379599 +0100
++++ PSMFeatureExtractor.xml	2021-02-06 18:39:07.710920755 +0100
+@@ -18,8 +18,12 @@
  
  ## Preprocessing
  mkdir in &&
-+#if $in
- ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
-+#else if $in_single
-+    ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&  
++#if $in_single
++    ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&
++#else
+ mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+ ${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 +#end if
  mkdir out &&
  
  ## Main program call
-@@ -27,7 +31,11 @@
+@@ -29,7 +33,11 @@
  python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
  @EXECUTABLE@ -ini @EXECUTABLE@.ctd
  -in
-+#if $in
- ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
-+#else if $in_single
++#if $in_single
 +'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)'
++#else
+ ${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 +#end if
  -out
  'out/output.${out_type}'
  
-@@ -41,7 +49,8 @@
+@@ -43,7 +51,8 @@
      <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
    </configfiles>
    <inputs>
 -    <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
-+   <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
++    <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
 +    <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/>   
      <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
        <option value="idXML">idxml</option>
diff --git a/tools/openms/PSMFeatureExtractor.xml b/tools/openms/PSMFeatureExtractor.xml
index 7d0cad983..58f7c80af 100644
--- a/tools/openms/PSMFeatureExtractor.xml
+++ b/tools/openms/PSMFeatureExtractor.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy2" profile="20.05">
+<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Computes extra features for each input PSM.</description>
   <macros>
     <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
@@ -14,13 +14,15 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-#if $in
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
-#else if $in_single
-    ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&  
+#if $in_single
+    ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&
+#else
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #end if
 mkdir out &&
 
@@ -31,10 +33,10 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-#if $in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
-#else if $in_single
+#if $in_single
 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)'
+#else
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #end if
 -out
 'out/output.${out_type}'
@@ -49,7 +51,7 @@ ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2om
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-   <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
+    <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
     <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/>   
     <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="idXML">idxml</option>
diff --git a/tools/openms/PTModel.xml b/tools/openms/PTModel.xml
index 20cbbc2b6..69b478ea7 100644
--- a/tools/openms/PTModel.xml
+++ b/tools/openms/PTModel.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_positive &&
diff --git a/tools/openms/PeakPickerHiRes.xml b/tools/openms/PeakPickerHiRes.xml
index f49265bc5..160ab7ad6 100644
--- a/tools/openms/PeakPickerHiRes.xml
+++ b/tools/openms/PeakPickerHiRes.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PeakPickerIterative.xml b/tools/openms/PeakPickerIterative.xml
index 43b290183..d79edc35f 100644
--- a/tools/openms/PeakPickerIterative.xml
+++ b/tools/openms/PeakPickerIterative.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PeakPickerWavelet.xml b/tools/openms/PeakPickerWavelet.xml
index 018415568..5d924478d 100644
--- a/tools/openms/PeakPickerWavelet.xml
+++ b/tools/openms/PeakPickerWavelet.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PepNovoAdapter.patch b/tools/openms/PepNovoAdapter.patch
index 9e7a18036..2ad5ddaf9 100644
--- a/tools/openms/PepNovoAdapter.patch
+++ b/tools/openms/PepNovoAdapter.patch
@@ -1,6 +1,6 @@
 --- PepNovoAdapter.xml	2020-05-12 15:55:24.712831518 +0200
 +++ /tmp/PepNovoAdapter.xml	2020-05-12 15:36:31.267276757 +0200
-@@ -42,8 +42,13 @@
+@@ -43,8 +43,13 @@
    </configfiles>
    <inputs>
      <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
@@ -16,7 +16,7 @@
      </param>
      <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/>
      <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/>
-@@ -51,8 +56,14 @@
+@@ -52,8 +57,14 @@
      <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/>
      <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/>
      <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/>
diff --git a/tools/openms/PepNovoAdapter.xml b/tools/openms/PepNovoAdapter.xml
index 8199d541b..07af2a758 100644
--- a/tools/openms/PepNovoAdapter.xml
+++ b/tools/openms/PepNovoAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PeptideIndexer.xml b/tools/openms/PeptideIndexer.xml
index 339bd6f0d..d8b788fd0 100644
--- a/tools/openms/PeptideIndexer.xml
+++ b/tools/openms/PeptideIndexer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PercolatorAdapter.xml b/tools/openms/PercolatorAdapter.xml
index e394207b7..86e211a43 100644
--- a/tools/openms/PercolatorAdapter.xml
+++ b/tools/openms/PercolatorAdapter.xml
@@ -14,15 +14,18 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+  mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+  ${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #end if
 #if $in_decoy:
   mkdir in_decoy &&
-  ${ ' '.join(["ln -s '%s' 'in_decoy/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _]) }
+  mkdir ${' '.join(["'in_decoy/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_decoy if _])} && 
+  ${' '.join(["ln -s '%s' 'in_decoy/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _])}
 #end if
 #if $in_osw:
   mkdir in_osw &&
@@ -66,11 +69,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 #if $in:
   -in
-  ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+  ${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #end if
 #if $in_decoy:
   -in_decoy
-  ${' '.join(["'in_decoy/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _])}
+  ${' '.join(["'in_decoy/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_decoy if _])}
 #end if
 #if $in_osw:
   -in_osw
diff --git a/tools/openms/PhosphoScoring.xml b/tools/openms/PhosphoScoring.xml
index 84f65d81e..b1c42eb50 100644
--- a/tools/openms/PhosphoScoring.xml
+++ b/tools/openms/PhosphoScoring.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PrecursorIonSelector.xml b/tools/openms/PrecursorIonSelector.xml
index c7d9e46dd..cf329b98e 100644
--- a/tools/openms/PrecursorIonSelector.xml
+++ b/tools/openms/PrecursorIonSelector.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/PrecursorMassCorrector.xml b/tools/openms/PrecursorMassCorrector.xml
index f39730368..b37690ba6 100644
--- a/tools/openms/PrecursorMassCorrector.xml
+++ b/tools/openms/PrecursorMassCorrector.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/ProteinInference.xml b/tools/openms/ProteinInference.xml
index 8b4b3f435..fefbf6c54 100644
--- a/tools/openms/ProteinInference.xml
+++ b/tools/openms/ProteinInference.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 
 ## Main program call
@@ -27,7 +29,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${gxy2omsext("idxml")}'
 
diff --git a/tools/openms/ProteinQuantifier.xml b/tools/openms/ProteinQuantifier.xml
index 3b5f9e7e6..029d51fe8 100644
--- a/tools/openms/ProteinQuantifier.xml
+++ b/tools/openms/ProteinQuantifier.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/ProteinResolver.xml b/tools/openms/ProteinResolver.xml
index 80eeb51d2..4a377de55 100644
--- a/tools/openms/ProteinResolver.xml
+++ b/tools/openms/ProteinResolver.xml
@@ -14,13 +14,15 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir fasta &&
 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
 #if $in:
   mkdir in &&
-  ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+  mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+  ${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #end if
 #if $design:
   mkdir design &&
@@ -49,7 +51,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)'
 #if $in:
   -in
-  ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+  ${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #end if
 #if $design:
   -design
diff --git a/tools/openms/QCCalculator.xml b/tools/openms/QCCalculator.xml
index 165e780f6..52e4fdd69 100644
--- a/tools/openms/QCCalculator.xml
+++ b/tools/openms/QCCalculator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/QCEmbedder.xml b/tools/openms/QCEmbedder.xml
index 40d13ff35..50150c7ed 100644
--- a/tools/openms/QCEmbedder.xml
+++ b/tools/openms/QCEmbedder.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/QCExporter.xml b/tools/openms/QCExporter.xml
index 0fcc82ab1..fdc23454a 100644
--- a/tools/openms/QCExporter.xml
+++ b/tools/openms/QCExporter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/QCExtractor.xml b/tools/openms/QCExtractor.xml
index 7bde3ecb4..0c99fcb25 100644
--- a/tools/openms/QCExtractor.xml
+++ b/tools/openms/QCExtractor.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/QCImporter.xml b/tools/openms/QCImporter.xml
index ff8959076..b366278b9 100644
--- a/tools/openms/QCImporter.xml
+++ b/tools/openms/QCImporter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/QCMerger.xml b/tools/openms/QCMerger.xml
index a875b5a10..9d008bcac 100644
--- a/tools/openms/QCMerger.xml
+++ b/tools/openms/QCMerger.xml
@@ -14,10 +14,12 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir out &&
 
 ## Main program call
@@ -27,7 +29,7 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -out
 'out/output.${gxy2omsext("qcml")}'
 
diff --git a/tools/openms/QCShrinker.xml b/tools/openms/QCShrinker.xml
index 2e4d8fdc8..f97c0e1ab 100644
--- a/tools/openms/QCShrinker.xml
+++ b/tools/openms/QCShrinker.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/QualityControl.xml b/tools/openms/QualityControl.xml
index 7755b0883..ae232abda 100644
--- a/tools/openms/QualityControl.xml
+++ b/tools/openms/QualityControl.xml
@@ -14,17 +14,20 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_cm &&
 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
 #if $in_raw:
   mkdir in_raw &&
-  ${ ' '.join(["ln -s '%s' 'in_raw/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _]) }
+  mkdir ${' '.join(["'in_raw/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_raw if _])} && 
+  ${' '.join(["ln -s '%s' 'in_raw/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _])}
 #end if
 #if $in_postFDR:
   mkdir in_postFDR &&
-  ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) }
+  mkdir ${' '.join(["'in_postFDR/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_postFDR if _])} && 
+  ${' '.join(["ln -s '%s' 'in_postFDR/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -34,6 +37,7 @@ ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy
 #end if
 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_feat &&
+  mkdir ${' '.join(["'out_feat/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_postFDR if _])} && 
 #end if
 #if $in_contaminants:
   mkdir in_contaminants &&
@@ -41,7 +45,8 @@ ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy
 #end if
 #if $in_trafo:
   mkdir in_trafo &&
-  ${ ' '.join(["ln -s '%s' 'in_trafo/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _]) }
+  mkdir ${' '.join(["'in_trafo/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_trafo if _])} && 
+  ${' '.join(["ln -s '%s' 'in_trafo/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _])}
 #end if
 
 ## Main program call
@@ -54,11 +59,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
 #if $in_raw:
   -in_raw
-  ${' '.join(["'in_raw/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _])}
+  ${' '.join(["'in_raw/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _])}
 #end if
 #if $in_postFDR:
   -in_postFDR
-  ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
+  ${' '.join(["'in_postFDR/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
@@ -70,7 +75,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 #end if
 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_feat
-  ${' '.join(["'out_feat/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in_postFDR if _])}
+  ${' '.join(["'out_feat/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in_postFDR if _])}
 #end if
 #if $in_contaminants:
   -in_contaminants
@@ -78,7 +83,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 #end if
 #if $in_trafo:
   -in_trafo
-  ${' '.join(["'in_trafo/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _])}
+  ${' '.join(["'in_trafo/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _])}
 #end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
@@ -92,7 +97,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
   && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
 #end if
 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  ${' '.join(["&& mv -n 'in_postFDR/%(id)s.%(gext)s' 'out_feat/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $out_feat if _])}
+  ${' '.join(["&& mv -n 'out_feat/%(bn)s/%(id)s.%(gext)s' 'out_feat/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $in_postFDR if _])}
 #end if
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
@@ -140,7 +145,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
       <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
     <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat">
-      <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/>
+      <discover_datasets directory="out_feat" recurse="true" format="featurexml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
diff --git a/tools/openms/RNADigestor.xml b/tools/openms/RNADigestor.xml
index 41a52bed6..4a9c0bafb 100644
--- a/tools/openms/RNADigestor.xml
+++ b/tools/openms/RNADigestor.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/RNAMassCalculator.xml b/tools/openms/RNAMassCalculator.xml
index 0f10510b4..7e52f45df 100644
--- a/tools/openms/RNAMassCalculator.xml
+++ b/tools/openms/RNAMassCalculator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/RNPxlSearch.xml b/tools/openms/RNPxlSearch.xml
index 984c525e1..7d61d6220 100644
--- a/tools/openms/RNPxlSearch.xml
+++ b/tools/openms/RNPxlSearch.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/RNPxlXICFilter.xml b/tools/openms/RNPxlXICFilter.xml
index 7526f69d9..ee2e0982b 100644
--- a/tools/openms/RNPxlXICFilter.xml
+++ b/tools/openms/RNPxlXICFilter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir control &&
diff --git a/tools/openms/RTEvaluation.xml b/tools/openms/RTEvaluation.xml
index 8964fd52e..ed298f409 100644
--- a/tools/openms/RTEvaluation.xml
+++ b/tools/openms/RTEvaluation.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/RTModel.xml b/tools/openms/RTModel.xml
index 5d5d2f2fd..952e9ed45 100644
--- a/tools/openms/RTModel.xml
+++ b/tools/openms/RTModel.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/SeedListGenerator.xml b/tools/openms/SeedListGenerator.xml
index 5fe28ed72..0894d366c 100644
--- a/tools/openms/SeedListGenerator.xml
+++ b/tools/openms/SeedListGenerator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SemanticValidator.xml b/tools/openms/SemanticValidator.xml
index 0afad65fe..7fd55819e 100644
--- a/tools/openms/SemanticValidator.xml
+++ b/tools/openms/SemanticValidator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
@@ -22,7 +23,8 @@ mkdir mapping_file &&
 ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' &&
 #if $cv:
   mkdir cv &&
-  ${ ' '.join(["ln -s '%s' 'cv/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _]) }
+  mkdir ${' '.join(["'cv/%s'"%(os.path.basename(str(_))[:-4]) for _ in $cv if _])} && 
+  ${' '.join(["ln -s '%s' 'cv/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])}
 #end if
 
 ## Main program call
@@ -37,7 +39,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)'
 #if $cv:
   -cv
-  ${' '.join(["'cv/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])}
+  ${' '.join(["'cv/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])}
 #end if
 | tee '$stdout'
 
diff --git a/tools/openms/SequenceCoverageCalculator.xml b/tools/openms/SequenceCoverageCalculator.xml
index 7b4f2651a..cba2f5d75 100644
--- a/tools/openms/SequenceCoverageCalculator.xml
+++ b/tools/openms/SequenceCoverageCalculator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_database &&
diff --git a/tools/openms/SimpleSearchEngine.xml b/tools/openms/SimpleSearchEngine.xml
index d0aae6c14..ac1b6a591 100644
--- a/tools/openms/SimpleSearchEngine.xml
+++ b/tools/openms/SimpleSearchEngine.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SiriusAdapter.xml b/tools/openms/SiriusAdapter.xml
index 5bf4e0099..0944628cd 100644
--- a/tools/openms/SiriusAdapter.xml
+++ b/tools/openms/SiriusAdapter.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
   <macros>
     <token name="@EXECUTABLE@">SiriusAdapter</token>
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpecLibCreator.xml b/tools/openms/SpecLibCreator.xml
index a42b27de6..f17a4d5e1 100644
--- a/tools/openms/SpecLibCreator.xml
+++ b/tools/openms/SpecLibCreator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir info &&
diff --git a/tools/openms/SpecLibSearcher.xml b/tools/openms/SpecLibSearcher.xml
index 586054792..0602ba2e9 100644
--- a/tools/openms/SpecLibSearcher.xml
+++ b/tools/openms/SpecLibSearcher.xml
@@ -14,13 +14,16 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
+${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 mkdir lib &&
 ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
 mkdir out &&
+mkdir ${' '.join(["'out/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && 
 
 ## Main program call
 
@@ -29,14 +32,14 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 -lib
 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)'
 -out
-${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("idxml")) for _ in $in if _])}
+${' '.join(["'out/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("idxml")) for _ in $in if _])}
 
 ## Postprocessing
-${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("idxml")} for _ in $out if _])}
+${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("idxml")} for _ in $in if _])}
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -5960,7 +5963,7 @@ ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]
   </inputs>
   <outputs>
     <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
-      <discover_datasets directory="out" format="idxml" pattern="__name__"/>
+      <discover_datasets directory="out" recurse="true" format="idxml" pattern="__name__"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
diff --git a/tools/openms/SpectraFilterBernNorm.xml b/tools/openms/SpectraFilterBernNorm.xml
index 1eadbc58b..1373f4ba1 100644
--- a/tools/openms/SpectraFilterBernNorm.xml
+++ b/tools/openms/SpectraFilterBernNorm.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterMarkerMower.xml b/tools/openms/SpectraFilterMarkerMower.xml
index 0d0b9149e..729762b2d 100644
--- a/tools/openms/SpectraFilterMarkerMower.xml
+++ b/tools/openms/SpectraFilterMarkerMower.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterNLargest.xml b/tools/openms/SpectraFilterNLargest.xml
index 747ba8437..1a477a000 100644
--- a/tools/openms/SpectraFilterNLargest.xml
+++ b/tools/openms/SpectraFilterNLargest.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterNormalizer.xml b/tools/openms/SpectraFilterNormalizer.xml
index 0f308b80e..fb526f24b 100644
--- a/tools/openms/SpectraFilterNormalizer.xml
+++ b/tools/openms/SpectraFilterNormalizer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterParentPeakMower.xml b/tools/openms/SpectraFilterParentPeakMower.xml
index 76a126054..ba2145604 100644
--- a/tools/openms/SpectraFilterParentPeakMower.xml
+++ b/tools/openms/SpectraFilterParentPeakMower.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterScaler.xml b/tools/openms/SpectraFilterScaler.xml
index eb7cce0e6..686b25a8f 100644
--- a/tools/openms/SpectraFilterScaler.xml
+++ b/tools/openms/SpectraFilterScaler.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterSqrtMower.xml b/tools/openms/SpectraFilterSqrtMower.xml
index 1e4fe65dc..260da0663 100644
--- a/tools/openms/SpectraFilterSqrtMower.xml
+++ b/tools/openms/SpectraFilterSqrtMower.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterThresholdMower.xml b/tools/openms/SpectraFilterThresholdMower.xml
index 503e7df1f..c9bd0bbbc 100644
--- a/tools/openms/SpectraFilterThresholdMower.xml
+++ b/tools/openms/SpectraFilterThresholdMower.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraFilterWindowMower.xml b/tools/openms/SpectraFilterWindowMower.xml
index 67923a233..019f0c577 100644
--- a/tools/openms/SpectraFilterWindowMower.xml
+++ b/tools/openms/SpectraFilterWindowMower.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraMerger.xml b/tools/openms/SpectraMerger.xml
index 718e4177e..052a12613 100644
--- a/tools/openms/SpectraMerger.xml
+++ b/tools/openms/SpectraMerger.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SpectraSTSearchAdapter.xml b/tools/openms/SpectraSTSearchAdapter.xml
index 07c450b98..3b9f6fc06 100644
--- a/tools/openms/SpectraSTSearchAdapter.xml
+++ b/tools/openms/SpectraSTSearchAdapter.xml
@@ -14,11 +14,14 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir spectra_files &&
-${ ' '.join(["ln -s '%s' 'spectra_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _]) }
+mkdir ${' '.join(["'spectra_files/%s'"%(os.path.basename(str(_))[:-4]) for _ in $spectra_files if _])} && 
+${' '.join(["ln -s '%s' 'spectra_files/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])}
 mkdir output_files &&
+mkdir ${' '.join(["'output_files/%s'"%(os.path.basename(str(_))[:-4]) for _ in $spectra_files if _])} && 
 mkdir library_file &&
 ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
 #if $sequence_database_file:
@@ -43,9 +46,9 @@ set -o pipefail &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -spectra_files
-${' '.join(["'spectra_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])}
+${' '.join(["'spectra_files/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])}
 -output_files
-${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $output_files_type) for _ in $spectra_files if _])}
+${' '.join(["'output_files/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $output_files_type) for _ in $spectra_files if _])}
 -library_file
 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)'
 #if $sequence_database_file:
@@ -64,7 +67,7 @@ ${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier
 #end if
 
 ## Postprocessing
-${' '.join(["&& mv -n 'output_files/%(id)s.%(omsext)s' 'output_files/%(id)s.%(gext)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for _ in $spectra_files if _])}
+${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn)s/%(id)s.%(gext)s'"%{"bn": os.path.basename(str(_))[:-4], "id": re.sub('[^\w\-_]', '_', _.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for _ in $spectra_files if _])}
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -105,7 +108,7 @@ ${' '.join(["&& mv -n 'output_files/%(id)s.%(omsext)s' 'output_files/%(id)s.%(ge
   </inputs>
   <outputs>
     <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
-      <discover_datasets directory="output_files" pattern="__name_and_ext__"/>
+      <discover_datasets directory="output_files" recurse="true" pattern="__name_and_ext__"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
diff --git a/tools/openms/StaticModification.xml b/tools/openms/StaticModification.xml
index b62fce3a6..0ba81564b 100644
--- a/tools/openms/StaticModification.xml
+++ b/tools/openms/StaticModification.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/SvmTheoreticalSpectrumGeneratorTrainer.xml b/tools/openms/SvmTheoreticalSpectrumGeneratorTrainer.xml
index c15729004..d27f92a8c 100644
--- a/tools/openms/SvmTheoreticalSpectrumGeneratorTrainer.xml
+++ b/tools/openms/SvmTheoreticalSpectrumGeneratorTrainer.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in_spectra &&
diff --git a/tools/openms/TICCalculator.xml b/tools/openms/TICCalculator.xml
index b0d96effe..630fc842c 100644
--- a/tools/openms/TICCalculator.xml
+++ b/tools/openms/TICCalculator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/TOFCalibration.xml b/tools/openms/TOFCalibration.xml
index f945c83fe..701f92ece 100644
--- a/tools/openms/TOFCalibration.xml
+++ b/tools/openms/TOFCalibration.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/TargetedFileConverter.xml b/tools/openms/TargetedFileConverter.xml
index 24fc1f608..651ac017b 100644
--- a/tools/openms/TargetedFileConverter.xml
+++ b/tools/openms/TargetedFileConverter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/TextExporter.xml b/tools/openms/TextExporter.xml
index 9c5e9a9c1..2cb0a54de 100644
--- a/tools/openms/TextExporter.xml
+++ b/tools/openms/TextExporter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/TransformationEvaluation.xml b/tools/openms/TransformationEvaluation.xml
index 820c3f10d..ebd35287b 100644
--- a/tools/openms/TransformationEvaluation.xml
+++ b/tools/openms/TransformationEvaluation.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/XFDR.xml b/tools/openms/XFDR.xml
index 1b110692d..a28ae90fb 100644
--- a/tools/openms/XFDR.xml
+++ b/tools/openms/XFDR.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 #if $in:
diff --git a/tools/openms/XMLValidator.xml b/tools/openms/XMLValidator.xml
index 9dd571b6d..ef3f1bedf 100644
--- a/tools/openms/XMLValidator.xml
+++ b/tools/openms/XMLValidator.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/XTandemAdapter.xml b/tools/openms/XTandemAdapter.xml
index e7f049cba..2f9b1e6ce 100644
--- a/tools/openms/XTandemAdapter.xml
+++ b/tools/openms/XTandemAdapter.xml
@@ -14,6 +14,7 @@
   <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
+#import os.path
 
 ## Preprocessing
 mkdir in &&
diff --git a/tools/openms/macros_autotest.xml b/tools/openms/macros_autotest.xml
index b6a35923f..55dba7e88 100644
--- a/tools/openms/macros_autotest.xml
+++ b/tools/openms/macros_autotest.xml
@@ -27186,4 +27186,4 @@
       </output>
     </test>
   </xml>
-<xml name="autotest_InspectAdapter"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_RTPredict"/><xml name="autotest_PTPredict"/><xml name="autotest_IDDecoyProbability"/></macros>
+<xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_InspectAdapter"/><xml name="autotest_PTPredict"/><xml name="autotest_RTPredict"/><xml name="autotest_IDDecoyProbability"/></macros>
diff --git a/tools/openms/macros_test.xml b/tools/openms/macros_test.xml
index 96c7ffabf..806b151d8 100644
--- a/tools/openms/macros_test.xml
+++ b/tools/openms/macros_test.xml
@@ -266,17 +266,16 @@
     <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
     <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
     <output_collection name="output_files" count="1">
-      <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
     </output_collection>
   </test>
-  
   <!-- test with two inputs (actually the same file .. symlinked) -->
   <test>
     <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
     <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
     <output_collection name="output_files" count="2">
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
+      <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
     </output_collection>
   </test>
 </xml>
@@ -357,7 +356,7 @@
   </test>
   <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
     <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
+    <param name="in_single" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
     <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
     <param name="out_type" value="idxml"/>
     <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
diff --git a/tools/openms/readme.md b/tools/openms/readme.md
index 0390481ee..012242379 100644
--- a/tools/openms/readme.md
+++ b/tools/openms/readme.md
@@ -74,10 +74,15 @@ The tools work by:
 
 Preprocessing:
 
-- For each input / output data set parameter a directory is crated (named by
-  the parameter)
 - For input data set parameters the links to the actual location of the data
-  sets are created
+  sets are created, the link names are `element_identifier`.`EXT`, where `EXT`
+  is an extension that is known by OpenMS
+- In order to avoid name collisions for the created links each is placed in a
+  unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name
+  of the parameter and `DATASET_ID` is the id of the Galaxy dataset 
+- the same happens for output parameters that are in 1:1 correspondence with
+  an input parameter
+
 
 Main: